- absolute() - Method in class Tuple3d
-
- AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- AbsoluteValue() - Constructor for class AbsoluteValue
-
- accept(S, T) - Method in interface CheckedBiConsumer
-
Calls the function
- accept(S) - Method in interface CheckedConsumer
-
- accept(int) - Method in interface CheckedIntConsumer
-
- accept(int, int) - Method in interface Histogram.BinConsumer
-
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface AfterCondition
-
- accept(ObjectMask) - Method in class AndCondition
-
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface BeforeCondition
-
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class DistanceCondition
-
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in class IncreaseFeatureCondition
-
- accept(ObjectMask) - Method in class NeighborhoodCondition
-
- accept(ObjectMask) - Method in interface UpdatableBeforeCondition
-
- accept(ObjectMask) - Method in class WrapAsUpdatable
-
- accept(ParsedFilePathBag) - Method in class AtLeastZSlices
-
- accept(ParsedFilePathBag) - Method in class CheckParsedFilePathBag
-
- accept(Point2i, int) - Method in interface OffsettedPointTwoDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- accept(int, int, int) - Method in interface OffsettedScalarTwoDimensionalConsumer
-
Accepts a point
- accept(Point2i) - Method in interface PointTwoDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- accept(int, int, int) - Method in interface ScalarThreeDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- accept(int, int) - Method in interface ScalarTwoDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- acceptableProbability(AnnealScheme) - Method in class AssignMode
-
- acceptableProbability(AnnealScheme) - Method in class DirectAssignMode
-
- acceptableProbability(AnnealScheme) - Method in class TransformationAssignMode
-
- AcceptanceProbabilityCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
- AcceptanceProbabilityCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class AcceptanceProbabilityCalculator
-
- accepted() - Method in interface DualMarks
-
The accepted marks.
- acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in class AcceptIterationList
-
- acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in interface AcceptIterationPredicate
-
- acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in class RejectIterationIfAllHigh
-
- acceptIteration(BinaryVoxels<UnsignedByteBuffer>) - Method in class RejectIterationIfLowDisconnected
-
- AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.predicate
-
- AcceptIterationList() - Constructor for class AcceptIterationList
-
- AcceptIterationPredicate - Interface in org.anchoranalysis.image.voxel.object.morphological.predicate
-
A condition that must be fulfilled for a particular iteration of a morphological operation to be
accepted.
- acceptPathViaRegEx(Path, Pattern) - Static method in class MatchRegularExpression
-
- acceptProposal(ToDoubleFunction<T>) - Method in class OptimizationStep
-
- accepts(Class<?>) - Method in interface PropertyDefiner
-
- accepts(Class<?>) - Method in class SimplePropertyDefiner
-
- acceptsAsSource(Class<?>) - Method in class ExtractFromParam
-
Are the source-parameters acceptable for extraction? *
- AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale
-
Provides functions to provide access and creation to/from the object-mask representation of a
generic type.
- activateDebugMode(String) - Method in class ExecutionArguments
-
Activates debug-mode
- add(NamedBean<?>) - Method in class Define
-
Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine
a group where definitions are stored.
- add(PermutationSetter) - Method in class PermutationSetterList
-
- add(String) - Method in interface StringBeanCollection
-
- add(String) - Method in class StringList
-
- add(String) - Method in class StringSet
-
- add(Color) - Method in class ColorList
-
- add(RGBColor) - Method in class ColorList
-
- add(int, RGBColor) - Method in class ColorList
-
- add(NamedProvider<T>) - Method in class NamedProviderCombine
-
- add(String, T) - Method in class NameValueSet
-
- add(NameValue<T>) - Method in class NameValueSet
-
- add(NameValueSet<T>) - Method in class NameValueSet
-
- add(String, StoreSupplier<T>) - Method in class EagerEvaluationStore
-
- add(String, StoreSupplier<T>) - Method in class LazyEvaluationStore
-
- add(String, StoreSupplier<T>) - Method in interface NamedProviderStore
-
- add(StatefulMessageLogger) - Method in class MessageLoggerList
-
- add(Class<? extends InputFromManager>) - Method in class InputTypesExpected
-
- add(SubmittedJob) - Method in class ConcurrentJobMonitor
-
- add(Feature<? extends T>) - Method in class FeatureList
-
- add(double) - Method in class EnergyTotal
-
- add(String) - Method in class FeatureNameList
-
Adds a feature-name
- add(String, int) - Method in class FeatureNameMapToIndex
-
Adds a new featureName and index
- add(ResultsVector) - Method in class ResultsVectorList
-
- add(CacheTransferSource<? extends FeatureInput>) - Method in class CacheTransferSourceCollection
-
- add(String, Feature<T>) - Method in class NamedFeatureStore
-
Adds a named-feature to the store.
- add(BoundingBox) - Method in class BoundingBoxesOnPlane
-
- add(ObjectMask) - Method in class ObjectCollectionWithProperties
-
- add(ObjectWithProperties) - Method in class ObjectCollectionWithProperties
-
- add(Seed) - Method in class SeedCollection
-
- add(String, Stack) - Method in class NamedStacks
-
- add(String, StoreSupplier<Stack>) - Method in class NamedStacks
-
- add(String, Stack) - Method in class NamedStacksUniformSize
-
- add(String, StoreSupplier<TimeSequence>) - Method in class WrapStackAsTimeSequenceStore
-
- add(Stack) - Method in class TimeSequence
-
- add(RasterGenerator<T>) - Method in class CombineRasterGenerator
-
- add(ChannelEntry) - Method in class NamedEntries
-
- add(NamedChannelsForSeries) - Method in class NamedChannelsForSeriesConcatenate
-
- add(Stack) - Method in class StackSeries
-
- add(AcceptIterationPredicate) - Method in class AcceptIterationList
-
- add(ObjectMask) - Method in class ObjectCollection
-
- add(VoxelStatistics) - Method in class VoxelStatisticsCombined
-
- add(VoxelsWrapper) - Method in class VoxelsWrapperList
-
- add(String, Generator<T>) - Method in class CombinedListGenerator
-
- add(FileType[]) - Method in class ConcatenateFileTypes
-
- add(T) - Method in class OutputSequenceIncrementing
-
Outputs an additional element in the sequence.
- add(T, S) - Method in class OutputSequenceIndexed
-
Outputs an additional element in the sequence.
- add(T, Optional<S>) - Method in class OutputSequenceIndexed
-
Outputs an additional element in the sequence.
- add(OutputtedFile) - Method in class RootDirectory
-
- add(MutableDirectory) - Method in class RootDirectory
-
- add(OutputtedFile) - Method in class Subdirectory
-
- add(String, boolean) - Method in class RecordedOutputs
-
Adds a new output-name to the set of recorded names.
- add(int, long) - Method in class VarianceCalculator
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
-
- add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class MarksWithEnergyBreakdown
-
- add(VoxelizedMarkMemo) - Method in class MarksWithTotalEnergy
-
- add(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class VoxelizedMarksWithEnergy
-
- add(EnergyTotal) - Method in class EnergySavedInd
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs
-
- add(String, EnergyScheme) - Method in class EnergySchemeSet
-
- add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParams, EnergySchemeWithSharedFeatures) - Method in class EnergyMemoList
-
- add(VoxelizedMarkMemo) - Method in class MemoList
-
- add(UpdatableMarks) - Method in class UpdatableMarksList
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList
-
- add(MemoForIndex) - Method in class UpdatableMarksList
-
- add(int, UpdatableMarks) - Method in class UpdatableMarksList
-
- add(IndexByRegion<T>) - Method in class IndexByChannel
-
- add(String, StoreSupplier<T>) - Method in interface MultiInputSubMap
-
Adds an entry to the map
- add(String, StoreSupplier<T>) - Method in class OperationMap
-
- add(String, StoreSupplier<TimeSequence>) - Method in class StackWithMap
-
- add(Mark, Color) - Method in class ColoredMarks
-
- add(Mark, RGBColor) - Method in class ColoredMarks
-
- add(Mark) - Method in class MarkCollection
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks
-
- add(String) - Method in class ErrorNode
-
- add(Exception) - Method in class ErrorNode
-
- add(String) - Method in class ErrorNodeImpl
-
- add(Exception) - Method in class ErrorNodeImpl
-
- add(String) - Method in class ErrorNodeNull
-
- add(Exception) - Method in class ErrorNodeNull
-
- add(FeedbackReceiver<T>) - Method in class FeedbackReceiverList
-
- add(TerminationCondition) - Method in class TerminationConditionListOr
-
- add(WeightedKernel<T, S>) - Method in class WeightedKernelList
-
- add(AggregateReceiver<T>) - Method in class AggregateReceiverList
-
- add(PeriodReceiver<T>) - Method in class PeriodReceiverList
-
- add(Overlay, RGBColor) - Method in class ColoredOverlayCollection
-
- add(Overlay) - Method in class OverlayCollection
-
- add(String, String) - Method in class OverlayProperties
-
- add(String, int) - Method in class OverlayProperties
-
- add(double) - Method in class AxisLimits
-
- add(AnnotationGroup<T>) - Method in class AnnotationGroupList
-
- add(double) - Method in class RangeSum
-
- add(LabelledWithConfidence<ObjectMask>) - Method in class SegmentedObjects
-
Adds a single object.
- add(String, Collection<WithConfidence<ObjectMask>>) - Method in class SegmentedObjects
-
Adds one or more objects with an identical class-label.
- add(LevelResult) - Method in class LevelResultCollection
-
- add(S, T) - Method in interface AddToAggregateItem
-
- add(Optional<String>, String, S) - Method in class GroupMapByName
-
Adds an item with an identifier
- add(T, String) - Method in class FileLabelMap
-
- add(NamedChannelsInput) - Method in class ImageSize
-
- add(NamedChannelsInput) - Method in class SummarizerNamedChannelsSimple
-
- add(T) - Method in class SummarizerInputFromManager
-
- add(Path) - Method in class ExtensionCount
-
- add(Path) - Method in class FilePathPattern
-
- add(Path) - Method in class FileSizeStatistics
-
- add(T) - Method in class Summarizer
-
Adds a element to the summary.
- add(T) - Method in class SummarizerAggregate
-
- add(T) - Method in class SummarizerCount
-
- add(T) - Method in class SummarizerListMultiline
-
- add(T) - Method in class SummarizerSplitMoreThan
-
- add(FileDetails) - Method in class ParsedFilePathBag
-
- add(int, String) - Method in class SortedSetChannel
-
- add(Point3i) - Method in class PointRange
-
- add(int, int, int) - Method in class PointRange
-
- add(Point2i) - Method in class Point2d
-
- add(Point2d) - Method in class Point2d
-
- add(Point2i) - Method in class Point2i
-
- add(Tuple3d) - Method in class Tuple3d
-
- add(double, double, double) - Method in class Tuple3d
-
- add(ReadableTuple3i) - Method in class Tuple3d
-
- add(ReadableTuple3i) - Method in class Tuple3i
-
- add(BoundingBox, T) - Method in class RTree
-
Adds a bounding-box with a corresponding index.
- addAcceptedAnnotation(T) - Method in interface AddAnnotation
-
- addAcceptedAnnotation(T) - Method in class AnnotationGroup
-
- addAcceptedAnnotation(T) - Method in class AnnotationGroupList
-
- addAcceptedAnnotation(AssignmentOverlapFromPairs) - Method in class AnnotationGroupObject
-
- addAdditionalOptions(Options) - Method in class LauncherConfig
-
- addAdditionalOptions(Options) - Static method in class CommandLineOptions
-
- addAll(Define) - Method in class Define
-
Adds all the named-beans (shallow copy) from source to th ecurrent map
- addAll(ColorList) - Method in class ColorList
-
- addAll(FeatureList<? extends T>) - Method in class FeatureList
-
- addAll(ObjectCollection) - Method in class ObjectCollection
-
- addAll(Collection<? extends ObjectMask>) - Method in class ObjectCollection
-
- addAll(MemoForIndex) - Method in class MemoList
-
- addAll(Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
-
- addAll(int, Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
-
- addAll(MarkCollection, RGBColor) - Method in class ColoredMarks
-
- addAll(ColoredMarks) - Method in class ColoredMarks
-
- addAll(MarkCollection) - Method in class MarkCollection
-
- addAll(OverlayCollection) - Method in class OverlayCollection
-
- addAll(Collection<AnnotationGroup<T>>) - Method in class AnnotationGroupList
-
- addAllOutputNamesTo(OutputEnabledMutable) - Method in class DefineOutputter
-
- addAllScaled(ColorList, double) - Method in class ColorList
-
- addAllToUpdatablePairList(UpdatableMarksList) - Method in class VoxelizedMarksWithEnergy
-
- AddAnnotation<T extends Assignment> - Interface in org.anchoranalysis.plugin.annotation.comparison
-
- addAsSeparateChannels(NamedStacks, int, Progress) - Method in interface NamedChannelsForSeries
-
- addAsSeparateChannels(NamedProviderStore<TimeSequence>, int) - Method in interface NamedChannelsForSeries
-
- addAsSeparateChannels(NamedStacks, int, Progress) - Method in class NamedChannelsForSeriesConcatenate
-
- addAsSeparateChannels(NamedProviderStore<TimeSequence>, int) - Method in class NamedChannelsForSeriesConcatenate
-
- addAsSeparateChannels(NamedStacks, int, Progress) - Method in class NamedChannelsForSeriesMap
-
- addAsSeparateChannels(NamedProviderStore<TimeSequence>, int) - Method in class NamedChannelsForSeriesMap
-
- addBasicOptions(Options) - Static method in class CommandLineOptions
-
- addBeansFromList(Define, List<NamedBean<?>>) - Static method in class DefineAdderUtilities
-
- addBlankChannel() - Method in class Stack
-
- addBoundChangeListener(BoundChangeListener) - Method in class BoundedIndexContainerFromList
-
- addBoundChangeListener(BoundChangeListener) - Method in interface BoundedRangeIncompleteDynamic
-
- addBoundChangeListener(BoundChangeListener) - Method in class BoundsFromRange
-
- addBoundChangeListener(BoundChangeListener) - Method in class BoundedIndexContainerBridge
-
- addBoundChangeListener(BoundChangeListener) - Method in class IntegerSequenceContaner
-
- addBoundChangeListener(BoundChangeListener) - Method in class SingleContainer
-
- addChangeID(Mark, Color) - Method in class ColoredMarks
-
- addChangeID(Mark, RGBColor) - Method in class ColoredMarks
-
- addChannel(Channel) - Method in class Stack
-
- addChannel(Channel) - Method in class StackNotUniformSized
-
- addChannelsFrom(Stack) - Method in class Stack
-
- AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- AddConstant() - Constructor for class AddConstant
-
- AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- AddConstantTo() - Constructor for class AddConstantTo
-
- AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria
-
Add Criteria
- AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class AddCriteriaEnergyPair
-
- AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
-
- AddCriteriaFeatureRelationThreshold() - Constructor for class AddCriteriaFeatureRelationThreshold
-
- AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaNever() - Constructor for class AddCriteriaNever
-
- AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaOr() - Constructor for class AddCriteriaOr
-
- AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaPair() - Constructor for class AddCriteriaPair
-
- addCustomNames(FeatureList<?>) - Method in class FeatureNameList
-
Add the customNames of a feature
- addCustomNamesWithPrefix(String, FeatureList<?>) - Method in class FeatureNameList
-
Add the customNames of a feature with a Prefix
- addDefaultOutputs(OutputEnabledMutable) - Method in class AnnotationComparisonAssigner
-
Adds any default outputs that should occur from the assigner.
- addDefaultOutputs(OutputEnabledMutable) - Method in class FeatureCostAssigner
-
- addDefaultOutputs(OutputEnabledMutable) - Method in class MaskIntersectionAssigner
-
- addDictionary(String, Dictionary) - Method in class ImageInitialization
-
Adds a dictionary to named-collection of dictionaries.
- AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define
-
Performs a Watershed on an EDT transform by bundling together several other beans
- AddDistanceTransform() - Constructor for class AddDistanceTransform
-
- addDoubleAsString(String, double) - Method in class OverlayProperties
-
- AddDualTransformer - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- AddDualTransformer() - Constructor for class AddDualTransformer
-
- addEdge(V, V) - Method in class GraphWithoutPayload
-
Add an edge between two vertices.
- addEdge(V, V, P) - Method in class GraphWithPayload
-
Add an edge between two vertices.
- AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define
-
- AddEdgeFilters() - Constructor for class AddEdgeFilters
-
- addEdges(V, Collection<V>) - Method in class GraphWithoutPayload
-
Adds edge(s) from the vertex from to each element in toCollection.
- addEnabledOutputFirst(String...) - Method in class OutputEnabledMutable
-
Adds enabled first-level outputs.
- addEnabledOutputs(OutputEnabledMutable) - Method in class OutputEnabledMutable
-
- addEnabledOutputSecond(String, String...) - Method in class OutputEnabledMutable
-
Adds enabled second-level outputs.
- AddEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- AddEnergy() - Constructor for class AddEnergy
-
- addErrorDescription(StringBuilder) - Method in class ErrorNode
-
- addErrorDescription(StringBuilder) - Method in class ErrorNodeImpl
-
- addErrorDescription(StringBuilder) - Method in class ErrorNodeNull
-
- addErrorLevel(String) - Method in class ProposerContext
-
- addField(Field) - Method in class PermutationSetterSingle
-
- addFormatted(String, Object...) - Method in class ErrorNode
-
- addFormatted(String, Object...) - Method in class ErrorNodeImpl
-
- addFormatted(String, Object...) - Method in class ErrorNodeNull
-
- addForSlice(int, int) - Method in interface VoxelPartition
-
- addForSlice(int, int) - Method in class VoxelPartitionHistogram
-
- addFrom(BeanInstanceMap) - Method in class BeanInstanceMap
-
Populates the entries from another BeanInstanceMap
- addFrom(List<NamedBean<?>>) - Method in class BeanInstanceMap
-
- addFrom(NamedProvider<Stack>) - Method in class NamedStacks
-
- addFrom(CommandLineExtracter, InputArguments) - Static method in class AddInputOptions
-
Adds options to change the inputs from the command-line.
- addFrom(CommandLineExtracter, OutputArguments) - Static method in class AddOutputOptions
-
Adds options to add/remove change the outputs the inputs from the command-line.
- addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class SharedFeatureMulti
-
- addFromWithPrefix(NamedProvider<Stack>, String) - Method in class NamedStacks
-
- addFromXmlFile(Path) - Method in class RootPathMap
-
Adds root-paths contained in a list of XML Beans in an xml file
- addHistogram(Histogram) - Method in class Histogram
-
- addIgnoreInfinity(double) - Method in class AxisLimits
-
- addInputOptions(Options) - Static method in class CommandLineOptions
-
- AddInputOptions - Class in org.anchoranalysis.launcher.options.process
-
Adds options relating to inputting from the command-line.
- addLabelToDataset(DefaultCategoryDataset, T, int, String, String) - Method in class BarPlot
-
- addLabelToDataset(DefaultBoxAndWhiskerCategoryDataset, T, int, String, String) - Method in class BoxPlot
-
- addLabelToDataset(S, T, int, String, String) - Method in class PlotIndexBaseCategorical
-
- addLeftObject(ObjectMask) - Method in class AssignmentOverlapFromPairs
-
- addLeftObjects(ObjectCollection) - Method in class AssignmentOverlapFromPairs
-
- addListOfBeansToCollection(String, HierarchicalConfiguration, Collection<T>, Object) - Static method in class HelperListUtilities
-
- addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
-
- addMultiple(RGBColor, int) - Method in class ColorList
-
- addNewPath(Point3i, Point3i) - Method in class VisitedVoxels
-
Adds a new path with a point
- addNoDuplicate(FeatureList<FeatureInput>) - Method in class SharedFeatureMulti
-
- addObjectsNoBoundingBoxChange(Collection<T>) - Method in class BoundedList
-
Adds elements without changing the bounding-box
- addObjectsToGraph(ObjectCollection) - Method in class MergeGraph
-
- addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class ColoredObjectCollection
-
- addOperationRecorder(WriteOperationRecorder) - Method in class Outputter
-
- addOperationRecorder(WriteOperationRecorder) - Method in class OutputterChecked
-
Adds an additional operation recorder alongside any existing recorders.
- addOptionsFromCommandLine() - Method in class AddInputOptions
-
- AddOptionsFromCommandLine<T> - Class in org.anchoranalysis.launcher.options.process
-
Base class for adding options from command-line arguments.
- AddOptionsFromCommandLine(CommandLineExtracter, T) - Constructor for class AddOptionsFromCommandLine
-
- addOptionsFromCommandLine() - Method in class AddOptionsFromCommandLine
-
Maybe add options to the arguments from the command-line.
- addOptionsFromCommandLine() - Method in class AddOutputOptions
-
- AddOutputOptions - Class in org.anchoranalysis.launcher.options.process
-
Adds options relating to outputting from the command-line.
- addPair(ObjectMask, ObjectMask, double) - Method in class AssignmentOverlapFromPairs
-
- addProperties(NameValueSet<String>) - Method in class Orientation
-
- addProperties(NameValueSet<String>) - Method in class Orientation2D
-
- addProperties(NameValueSet<String>) - Method in class Orientation3DEulerAngles
-
- addProperties(NameValueSet<String>) - Method in class OrientationIdentity
-
- addPropertiesToMask(ObjectWithProperties) - Method in class Orientation
-
- addPropertiesToMask(ObjectWithProperties) - Method in class Orientation2D
-
- addPropertiesToMask(ObjectWithProperties) - Method in class Orientation3DEulerAngles
-
- addPropertiesToMask(ObjectWithProperties) - Method in class OrientationIdentity
-
- addResultsFor(RowLabels, ResultsVector) - Method in class GroupWriter
-
Adds a result to the group-writer, but doesn't write yet.
- addResultsFor(RowLabels, ResultsVector) - Method in class ResultsWriter
-
Adds feature-calculation results to be written.
- addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in interface ExportFeatureResultsAdder
-
Adds labeled results (which makes a row in a feature-table, and possibly other outputs).
- addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in class InputProcessContext
-
- addRightObject(ObjectMask) - Method in class AssignmentOverlapFromPairs
-
- addRightObjects(ObjectCollection) - Method in class AssignmentOverlapFromPairs
-
- addRow(RowLabels, ResultsVector) - Method in class FeatureCSVWriter
-
Directly adds a row of feature-values.
- addRow(List<TypedValue>) - Method in class FeatureCSVWriter
-
Directly adds a row in the form of typed-values.
- addSharedObjectsDictionary(Optional<SharedObjects>, Optional<Dictionary>) - Method in class ImageInitialization
-
- addShift(ReadableTuple3i) - Method in class ContiguousVoxelPath
-
Adds a shift to each point (modifying the existing points in memory), and returns them as a
list
- addSkippedAnnotationImage() - Method in interface AddAnnotation
-
- addSkippedAnnotationImage() - Method in class AnnotationGroup
-
- addSkippedAnnotationImage() - Method in class AnnotationGroupList
-
- addSlice(VoxelBuffer<T>) - Method in interface ProjectableBuffer
-
Adds a slice to the buffer.
- addStack(Provider<Stack>) - Method in class ArrangeRaster
-
Adds a stack to the existing list of stack-providers.
- addTo(Define) - Method in class Concatenate
-
- addTo(Define) - Method in interface DefineAdder
-
- addTo(Define) - Method in class FromXmlList
-
- addTo(ObjectMask, int) - Method in interface VoxelsArithmetic
-
Adds a constant-value to each voxel but only for voxels inside an object-mask
- addTo(Define) - Method in class AddDistanceTransform
-
- addTo(S, T) - Method in class GroupMapByName
-
- addTo(Define) - Method in class AddEdgeFilters
-
- addTo(Define) - Method in class VisualizeOnBackground
-
- AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped
-
Adds an individual-item to an aggregate-item
- AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules
-
Adds additional outputs-names to be enabled to the defaults.
- AddToDefaults() - Constructor for class AddToDefaults
-
- addToErrorNode(ErrorNode) - Method in exception ErrorNodeException
-
- addToManager(MultiInputManager, String, String) - Method in class FilePathBaseAppendToManager
-
- addToRow(List<TypedValue>) - Method in class RowLabels
-
Adds the identifiers to a row to be outputted in a features CSV.
- addToStacks(String, Stack) - Method in class ImageInitialization
-
- addToStacks(String, StackProvider) - Method in class ImageInitialization
-
- addToStore(NamedProviderStore<T>) - Method in interface MultiInputSubMap
-
- addToStore(NamedProviderStore<T>) - Method in class OperationMap
-
- addToStore(NamedProviderStore<TimeSequence>) - Method in class StackWithMap
-
- addToStore(NamedProviderStore<TimeSequence>, int, Progress) - Method in class StackWithMap
-
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class NamedChannelsInput
-
- addToStoreInferNames(NamedProviderStore<Stack>) - Method in interface ProvidesStackInput
-
Adds the current object to a named-store of stacks (using the default series)
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in interface ProvidesStackInput
-
Adds the current object to a named-store of stacks
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class MultiInput
-
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress) - Method in class ConvertNamedChannelsInputToStack
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class NamedChannelsInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in interface ProvidesStackInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class MultiInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress) - Method in class ConvertNamedChannelsInputToStack
-
- addToTypeValueCollection(Collection<TypedValue>, int) - Method in class ResultsVector
-
- addToUpdatablePairList(UpdatableMarksList, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
-
- addToVoxelList(int, int, int) - Method in class IndexByRegion
-
- addUnannotatedImage() - Method in interface AddAnnotation
-
- addUnannotatedImage() - Method in class AnnotationGroup
-
- addUnannotatedImage() - Method in class AnnotationGroupList
-
- addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
-
Adds job-manifests that don't have corresponding experiment-manifests.
- addUnused(T) - Method in interface VoxelPartitionFactory
-
- addUnused(Histogram) - Method in class VoxelPartitonFactoryHistogram
-
- addVertex(V) - Method in class GraphWithoutPayload
-
Adds a vertex.
- addVertex(V) - Method in class GraphWithPayload
-
Adds a vertex.
- addVisitedPoint(Point3i) - Method in class VisitedVoxels
-
Adds a visited-point to an existing path, or else makes a new one
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOption
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionDual
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionSingle
-
- addWithIndex(RGBColor) - Method in class ColorList
-
- addWithName(Define, String, AnchorBean<?>) - Method in class DefineAdderWithPrefixBean
-
- addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class OverlayProperties
-
- AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
-
- AdjacentFile() - Constructor for class AdjacentFile
-
- adjacentVerticesOutgoing(V) - Method in class GraphWithoutPayload
-
The vertices that are connected to a particular vertex by an outgoing edge.
- adjacentVerticesOutgoing(V) - Method in class GraphWithPayload
-
The vertices that are connected to a particular vertex by an outgoing edge.
- adjacentVerticesOutgoingStream(V) - Method in class GraphWithoutPayload
-
- adjacentVerticesOutgoingStream(V) - Method in class GraphWithPayload
-
- afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
-
- afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
-
- afterAllJobsAreExecuted(SharedState<T>, InputOutputContext) - Method in class CompareAnnotations
-
- afterAllJobsAreExecuted(SharedStateExportFeatures<S>, InputOutputContext) - Method in class ExportFeatures
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ConvertImageFormat
-
- afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class GroupedStackBase
-
- afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class ImageAssignLabel
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ScaleImage
-
- afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class SegmentInstanceWithModel
-
- afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class ExtractSlice
-
- afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class MovieFromSlices
-
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class CombineCSV
-
- afterAllJobsAreExecuted(RecordingCounter<T>, InputOutputContext) - Method in class CopyFiles
-
- afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class SummarizeBase
-
- afterAllJobsAreExecuted(SharedStateRememberConverted<U, S>, InputOutputContext) - Method in class ConvertNamedChannels
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportReportFeaturesFromManifest
-
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class ExportReportFeaturesFromMulti
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportObjectsAsCroppedImages
-
- afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class ExportObjectsFromCSV
-
- afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class SegmentMarksFromImage
-
- AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitScheduler
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerAnd
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerConvexAboutRoot
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerUniformSample
-
- aggEnd(Aggregator) - Method in interface AggregateReceiver
-
- aggEnd(Aggregator) - Method in class AggregateReceiverList
-
- aggEnd(Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggEnd(Aggregator) - Method in class CSVReporterAggregated
-
- aggEnd(Aggregator) - Method in class Log4JReporter
-
- aggEnd(Aggregator) - Method in class OptimizationStepLogReporter
-
- aggEnd(Aggregator) - Method in class TextFile
-
- AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggIDCounter(int) - Constructor for class AggIDCounter
-
- AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
-
Aggregates many per-image annotations together in form of a CSV file.
- AggregateAnnotations() - Constructor for class AggregateAnnotations
-
- AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateReceiverList() - Constructor for class AggregateReceiverList
-
- aggregateResults(List<Double>) - Method in class FeatureIntersectingObjectsSingleElement
-
- aggregateResults(List<Double>) - Method in class MaxFeatureIntersectingObjects
-
- aggregateResults(List<Double>) - Method in class MinFeatureIntersectingObjectsAboveThreshold
-
- aggregateResults(List<Double>) - Method in class NumberIntersectingObjectsAboveThreshold
-
- AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class AggregateTriggerBank
-
- Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- Aggregator(int) - Constructor for class Aggregator
-
- AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregatorException() - Constructor for exception AggregatorException
-
- AggregatorException(String) - Constructor for exception AggregatorException
-
- AggregatorException(Exception) - Constructor for exception AggregatorException
-
- aggReport(Reporting<T>, Aggregator) - Method in interface AggregateReceiver
-
- aggReport(Reporting<T>, Aggregator) - Method in class AggregateReceiverList
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
-
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface AggregateReceiver
-
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class AggregateReceiverList
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
-
- All - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed irrespective of outputName.
- All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects all possible channels from all possible stacks
- All() - Constructor for class All
-
- allAssociatedPaths() - Method in interface InputFromManager
-
- allChannelsAsStack(int) - Method in interface NamedChannelsForSeries
-
- allChannelsAsStack(int) - Method in class NamedChannelsForSeriesConcatenate
-
- allChannelsAsStack(int) - Method in class NamedChannelsForSeriesMap
-
- allChannelsHaveIdenticalType() - Method in class Stack
-
Determines if all channels have an identical voxel data-type.
- allChannelsHaveType(VoxelDataType) - Method in class RGBStack
-
- allChannelsHaveType(VoxelDataType) - Method in class Stack
-
Determines if all channels have a specific data-type.
- allChannelsHaveType(VoxelDataType) - Method in class TimeSequence
-
- allExtensions() - Method in enum ImageFileFormat
-
All extensions associated with a file-format.
- allFileTypes() - Method in class ConcatenateFileTypes
-
- allHeaders() - Method in class LabelHeaders
-
The non-group and group headers combined (in this order respectively)
- allImageExtensions() - Static method in class FormatExtensions
-
- allLabels(NoSharedState) - Method in class BinaryOutcomeImageLabeller
-
- allLabels(ImageCSVLabellerInitialization) - Method in class ImageCSVLabeller
-
- allLabels(T) - Method in class ImageLabeller
-
A set of identifiers for all groups that can be outputted by the labeller.
- allLabels(ImageLabellerStringMapInitialization<T>) - Method in class ImageLabellerStringMap
-
- allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class IterateVoxelsObjectMask
-
Do all points on an object-mask match a predicate on the point's voxel-intensity?
- allocate(int) - Static method in class UnsignedByteBuffer
-
Allocates a new buffer of unsigned-bytes.
- allocate(int) - Static method in class UnsignedIntBuffer
-
Allocates a new (direct) buffer of unsigned-ints.
- allocate(int) - Static method in class UnsignedShortBuffer
-
Allocates a new (direct) buffer of unsigned-shorts.
- allocateBuffer() - Method in class ToUnsignedByte
-
- allocateFloat(int) - Static method in class VoxelBufferFactory
-
Allocates a new float voxel-buffers of given size.
- allocateFloatArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of float voxel-buffers of given size.
- allocateUnsignedByte(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned byte voxel-buffer of given size.
- allocateUnsignedByteArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned byte voxel-buffers of given size.
- allocateUnsignedInt(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned int voxel-buffers of given size.
- allocateUnsignedIntArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned int voxel-buffers of given size.
- allocateUnsignedShort(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned short voxel-buffers of given size.
- allocateUnsignedShortArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned short voxel-buffers of given size.
- AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
- allSlices(Voxels<U>, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class Wrap
-
- AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Only takes pixels where indexNonZero has a nonzero pixel
- AllSlicesMaskEverythingNonZero() - Constructor for class AllSlicesMaskEverythingNonZero
-
- AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Gets all slices where indexNonZero has at least one non-zero pixel in that slice
- AllSlicesMaskNonZero() - Constructor for class AllSlicesMaskNonZero
-
- allSuccessful() - Method in class TaskStatistics
-
Did all jobs execute and completely successfully?
- AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
-
- AllValuesOff() - Constructor for class AllValuesOff
-
- AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
-
Creates a new mask of particular dimensionality where all values are ON
- AllValuesOn() - Constructor for class AllValuesOn
-
- Always - Class in org.anchoranalysis.plugin.image.bean.object.match
-
Specifies a single object that will always be the "match" for whatever source object.
- Always() - Constructor for class Always
-
- always2D(String) - Static method in class OutputSequenceStackFactory
-
The stacks that are outputted are guaranteed to be two-dimensional.
- always2D(boolean) - Method in class StackWriteAttributes
-
- AlwaysAllowed - Class in org.anchoranalysis.io.output.writer
-
Allows every output, irrespective of whether the
OutputterChecked allows the output-name.
- AlwaysAllowed(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class AlwaysAllowed
-
- alwaysExecuteBeforeCallingLibrary() - Static method in class CVInit
-
This routine must always be executed at least once before calling any routines in the OpenCV
library
- AlwaysNew<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace
-
Always create a new session-input with no reuse or caching.
- AlwaysNew(CacheCreator) - Constructor for class AlwaysNew
-
Constructor with default means of creating a session-input
- AlwaysNew(CacheCreator, ChildCacheFinder) - Constructor for class AlwaysNew
-
- AnchorBean<F> - Class in org.anchoranalysis.bean
-
The base class of all beans used in
Anchor.
- AnchorBean() - Constructor for class AnchorBean
-
- AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
Base class for all Anchor-specific bean factories
- AnchorBeanFactory() - Constructor for class AnchorBeanFactory
-
- AnchorCheckedException - Exception in org.anchoranalysis.core.exception
-
A base class for all checked exceptions used on the Anchor platform
- AnchorCheckedException() - Constructor for exception AnchorCheckedException
-
- AnchorCheckedException(String, Throwable) - Constructor for exception AnchorCheckedException
-
- AnchorCheckedException(String) - Constructor for exception AnchorCheckedException
-
- AnchorCheckedException(Throwable) - Constructor for exception AnchorCheckedException
-
- AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable
-
An exception that can be combined with similar exceptions and summarized.
- AnchorCombinableException(String, Throwable) - Constructor for exception AnchorCombinableException
-
- AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
The default bean factory used for initializing AnchorBeans
- AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class AnchorDefaultBeanFactory
-
- AnchorFriendlyCheckedException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular checked-exceptions which are guaranteed to provide a user-friendly
error description.
- AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception AnchorFriendlyCheckedException
-
A user-friendly error message and its cause.
- AnchorFriendlyCheckedException(String) - Constructor for exception AnchorFriendlyCheckedException
-
A user-friendly error message WITHOUT a cause.
- AnchorFriendlyCheckedException(Throwable) - Constructor for exception AnchorFriendlyCheckedException
-
A wrapped exception.
- AnchorFriendlyRuntimeException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly
error description.
- AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception AnchorFriendlyRuntimeException
-
A user-friendly error message and its cause.
- AnchorFriendlyRuntimeException(String) - Constructor for exception AnchorFriendlyRuntimeException
-
A user-friendly error message WITHOUT a cause.
- AnchorFriendlyRuntimeException(Throwable) - Constructor for exception AnchorFriendlyRuntimeException
-
A wrapped exception.
- AnchorImpossibleSituationException - Exception in org.anchoranalysis.core.exception.friendly
-
A run-time exception to throw in situations which should never occur, instead of
- AnchorImpossibleSituationException() - Constructor for exception AnchorImpossibleSituationException
-
- AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception
-
This is an exceotion that should never be thrown, but can be used for type-safety where an
exception is needed
- AnchorNeverOccursException() - Constructor for exception AnchorNeverOccursException
-
- AnchorRuntimeException - Exception in org.anchoranalysis.core.exception
-
A base class for all unchecked (runtime) exceptions used on the Anchor platform
- AnchorRuntimeException() - Constructor for exception AnchorRuntimeException
-
- AnchorRuntimeException(String, Throwable) - Constructor for exception AnchorRuntimeException
-
- AnchorRuntimeException(String) - Constructor for exception AnchorRuntimeException
-
- AnchorRuntimeException(Throwable) - Constructor for exception AnchorRuntimeException
-
- AnchorWebsiteLinks - Class in org.anchoranalysis.launcher
-
A centralized location for hyperlinks to the Anchor website.
- and(StackWriteAttributes) - Method in class StackWriteAttributes
-
- And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
- And() - Constructor for class And
-
- And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical AND i.e.
- And() - Constructor for class And
-
- AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
Combines two UpdatableBeforeConditions as LOGICAL ANDs
- AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class AndCondition
-
- AndKernel - Class in org.anchoranalysis.image.voxel.kernel
-
- AndKernel(BinaryKernel, BinaryKernel) - Constructor for class AndKernel
-
- AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- AndList() - Constructor for class AndList
-
- AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask
-
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
- AndObjectsWithMasks() - Constructor for class AndObjectsWithMasks
-
- AngleRotation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- AngleRotation() - Constructor for class AngleRotation
-
- AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
-
Perona-Malik Anisotropic Diffusion
- AnisotropicDiffusion() - Constructor for class AnisotropicDiffusion
-
- AnnealScheme - Class in org.anchoranalysis.mpp.bean
-
- AnnealScheme() - Constructor for class AnnealScheme
-
- Annotation - Interface in org.anchoranalysis.annotation
-
Base class for types of image annotations.
- AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
-
- AnnotationAggregateCSVGenerator() - Constructor for class AnnotationAggregateCSVGenerator
-
- AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean
-
- AnnotationBackground() - Constructor for class AnnotationBackground
-
- AnnotationComparisonAssigner<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
-
- AnnotationComparisonAssigner() - Constructor for class AnnotationComparisonAssigner
-
- AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
-
- AnnotationComparisonInput(T, Tuple2<Comparer, Comparer>, Tuple2<String, String>, StackReader) - Constructor for class AnnotationComparisonInput
-
- AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
- AnnotationComparisonInputManager() - Constructor for class AnnotationComparisonInputManager
-
- AnnotationDeleter - Interface in org.anchoranalysis.annotation.io
-
- annotationExistsCorrespondTo(Path) - Method in class MarkAnnotationReader
-
- AnnotationGroup<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
-
- AnnotationGroup(String) - Constructor for class AnnotationGroup
-
- AnnotationGroupList<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
-
- AnnotationGroupList() - Constructor for class AnnotationGroupList
-
- AnnotationGroupObject - Class in org.anchoranalysis.plugin.annotation.comparison
-
- AnnotationGroupObject(String) - Constructor for class AnnotationGroupObject
-
- AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean
-
- AnnotationInputManager() - Constructor for class AnnotationInputManager
-
- AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
-
- AnnotationLabel() - Constructor for class AnnotationLabel
-
- annotationLabelFor(ProvidesStackInput) - Method in class AnnotatorStrategy
-
Returns a label describing the annotation, or empty() if this makes no sense
- annotationLabelFor(ProvidesStackInput) - Method in class MarkProposerStrategy
-
- annotationLabelFor(ProvidesStackInput) - Method in class WholeImageLabelStrategy
-
- AnnotationMarksComparer<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparer
-
- AnnotationMarksComparer() - Constructor for class AnnotationMarksComparer
-
- annotationPathFor(ProvidesStackInput) - Method in class AnnotatorStrategy
-
- annotationPathFor(ProvidesStackInput) - Method in class SinglePathStrategy
-
- AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
-
- AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark
-
An image-annotation that involves a mark-collection.
- AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io
-
An annotation that has been combined with its strategy.
- AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class AnnotationWithStrategy
-
- AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
-
- AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean
-
- AnnotatorStrategy() - Constructor for class AnnotatorStrategy
-
- Anonymize - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Copies files to a number 001 002 etc.
- Anonymize() - Constructor for class Anonymize
-
- AnonymizeSharedState - Class in org.anchoranalysis.plugin.io.shared
-
- AnonymizeSharedState(NumberToStringConverter, Map<Integer, Integer>) - Constructor for class AnonymizeSharedState
-
- any() - Method in class VoxelsWrapper
-
Returns voxels that are not cast to any specific buffer type
- anyDimensionIsLargerThan(Extent) - Method in class Extent
-
Returns true if any dimension in this extent is larger than the corresponding dimension in
other extent
- anyExists() - Method in class PredicateAtCorner
-
- anyExists() - Method in class PredicateImplementation
-
- anyExists() - Method in interface VoxelsPredicate
-
Does at least one value satisfy the predicate - across all voxels?
- anyMatch(Predicate<ObjectMask>) - Method in class ObjectMaskStream
-
Does the predicate evaluate to true on any object in the collection?
- anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class IterateVoxelsAll
-
Tries to apply a predicate to all the remaining buffer locations, returning true if the
predicate matches.
- AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
The center ps of at least one slice should be on the stack Tries overall center point first, and
then projects it onto each slice
- AnySliceCenterOnMask() - Constructor for class AnySliceCenterOnMask
-
- append(Optional<FeatureList<T>>) - Method in class FeatureList
-
Appends one or more additional (optional) feature-lists
- AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A CSV that is appended from the root of a project
- AppendCsv() - Constructor for class AppendCsv
-
- AppendDictionary - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendDictionary() - Constructor for class AppendDictionary
-
- appendExtension(String, Optional<String>) - Static method in class ExtensionUtilities
-
Appends an (optional) extension to a string, adding in the leading period if the extension is
defined.
- appendExtension(Path, Optional<String>) - Static method in class ExtensionUtilities
-
- AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendFilePath() - Constructor for class AppendFilePath
-
- AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendHistogram() - Constructor for class AppendHistogram
-
- AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendMarks() - Constructor for class AppendMarks
-
- AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendObjects() - Constructor for class AppendObjects
-
- AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStack() - Constructor for class AppendStack
-
- AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStackDirect() - Constructor for class AppendStackDirect
-
- apply(Throwable, Writer, String, int, boolean) - Static method in class RecursivelyDescribeExceptionStack
-
Incrementally adds a line to a string builder with the message of each exception moving onto
the next nested exception until there are no more
- apply(S, T) - Method in interface CheckedBiFunction
-
Calls the function
- apply(S) - Method in interface CheckedFunction
-
Calls the function
- apply(int) - Method in interface CheckedIntFunction
-
Calls the function
- apply(T) - Method in interface CheckedUnaryOperator
-
- apply(int, int) - Method in interface IntBinaryOperation
-
- apply(Integer) - Method in class IndexBridge
-
- apply(ImageInitialization) - Static method in class CreateCombinedStack
-
- apply(Mask, Mask) - Static method in class MaskAnd
-
Performs a AND operation on each voxel in two masks, writing the result onto the second mask.
- apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class MaskAnd
-
Performs a AND operation on each voxel in two
Voxels (considered to be masks),
writing the result onto the second mask.
- apply(Mask, Mask) - Static method in class MaskIfHighLow
-
Performs a iff first==HIGH and second==LOW then LOW operation on each voxel in two
masks, writing the result onto the second mask.
- apply(Mask, Mask) - Static method in class MaskOr
-
Performs a OR operation on each voxel in two masks, writing the result onto the first mask.
- apply(Mask, Mask) - Static method in class MaskXor
-
Performs a XOR (exclusive OR) operation on each voxel in two masks, writing the result onto
the first mask.
- apply(BinaryVoxels<UnsignedByteBuffer>, BinaryVoxels<UnsignedByteBuffer>) - Static method in class MaskXor
-
Performs a XOR (exclusive OR) operation on each voxel in two
Voxels (considered to be
masks), writing the result onto the second mask.
- apply(List<ChannelEntry>) - Method in class NamedEntriesCreator
-
- apply(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as
voxels.
- apply(IFormatReader, ReadOptions, int) - Method in class DimensionsCreator
-
- apply(String, Path) - Static method in class WriteStringToFile
-
- applyAsDouble(T, U) - Method in interface CheckedToDoubleBiFunction
-
Applies this function to the given arguments.
- applyAsInt(S) - Method in interface CheckedToIntFunction
-
Calls the function
- applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class LinearLeastSquaresViaNormalEquationBase
-
- applyDelta(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta
-
Applies the changes to enable or disable additional outputs, if they are defined.
- applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class FitResult
-
- applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels and sums the returned value.
- applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels and sums the returned value.
- applyForCount(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
- applyGlobal(List<Point3i>) - Method in class OutlineTraverser
-
Root point is arbitrarily chosen from object
- applyGlobal(Point3i, List<Point3i>) - Method in class OutlineTraverser
-
- ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask
-
Applies an ImageJ (2D) morphological operation to voxels
- applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class PropertyInitializer
-
Applies the initialization to a property using the current or extracted params if possible.
- ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel
-
- applyMorphologicalOperation(Mask, boolean) - Method in class Dilate
-
- applyMorphologicalOperation(Mask, boolean) - Method in class Erode
-
- applyMorphologicalOperation(Mask, boolean) - Method in class MorphologicalOperatorBase
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Dilate
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Erode
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class ObjectCollectionProviderMorphological
-
- applyOperation(Dimensions, UnaryOperator<Stack>) - Method in class NamedStacks
-
Applies an operation on each stack in the collection and returns a new derived collection
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateIncrementalOperationMap
-
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateDilationMap
-
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateErosionMap
-
- applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class ApplyImageJMorphologicalOperation
-
- ApplyPermutations<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.permute
-
Applies a
PermuteProperty to a bean to create new duplicated beans each with a
permutation
- ApplyPermutations(ApplyPermutations.NameGetter<T>, ApplyPermutations.NameSetter<T>) - Constructor for class ApplyPermutations
-
- ApplyPermutations.NameGetter<S> - Interface in org.anchoranalysis.bean.permute
-
- ApplyPermutations.NameSetter<S> - Interface in org.anchoranalysis.bean.permute
-
- applyPermutationsToCreateDuplicates(List<T>, PermuteProperty<S>, PermutationSetter) - Method in class ApplyPermutations
-
Takes a list of beans, and creates a permuted version, updating the custom names
- applyRadiiSubtractScale(double, double) - Method in class FitResult
-
- applyRankFilter(Channel, int, int) - Static method in class FilterHelper
-
Applies a 2D rank-filter to each slice independently.
- applyStrategy(MergeCandidate) - Method in class MergeStrategy
-
- applyUntilPositive(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels until a positive value is returned, then exits with true.
- ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
-
Calculates deterministicly a point that is definitely inside the object-mask.
- ArbitraryInsidePoint(String) - Constructor for class ArbitraryInsidePoint
-
- ArbitraryInsidePoint() - Constructor for class ArbitraryInsidePoint
-
- ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria
-
If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
- ArbitraryPointCommon() - Constructor for class ArbitraryPointCommon
-
- Area<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
-
Area of the stack (XY dimensions only, Z dimension is not considered)
- Area() - Constructor for class Area
-
- areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class PointsNeighborChecker
-
Are all points in a list neighboring the next point in the list?
- AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
-
Area expressed in physical coordinates
- AreaPhysical() - Constructor for class AreaPhysical
-
- AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
-
Area expressed as square pixels
- AreaPixels(double) - Constructor for class AreaPixels
-
- AreaPixels() - Constructor for class AreaPixels
-
- areEqual(double, double) - Static method in class DoubleUtilities
-
Are the two numbers equal?
- areEqual(float, float) - Static method in class FloatUtilities
-
Are the two numbers equal?
- areNeighborsDistinct(List<Point3i>) - Static method in class PointsNeighborChecker
-
Makes sure no successive neighbors are equal
- arePointsNeighbors(Point3i, Point3i) - Static method in class PointsNeighborChecker
-
- areXmlEqual(Document, Document) - Static method in class TestLoader
-
Does a check if the XML documents are equal
- ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert
-
Converts string passed as arguments.
- arithmetic() - Method in class Channel
-
- arithmetic() - Method in class BoundedVoxels
-
- arithmetic() - Method in class Voxels
-
Methods to manipulate the voxel-values via arithmetic.
- arithmetic() - Method in class VoxelsWrapper
-
- ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
- ArithmeticWithConstantBase() - Constructor for class ArithmeticWithConstantBase
-
- ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- ArithmeticWithConstantConditionallyWriteBase() - Constructor for class ArithmeticWithConstantConditionallyWriteBase
-
- ArrangeRaster - Class in org.anchoranalysis.image.bean.provider.stack
-
Creates a stack that tiles (or otherwise combines) other providers
- ArrangeRaster(boolean, boolean) - Constructor for class ArrangeRaster
-
- ArrangeRaster() - Constructor for class ArrangeRaster
-
- ArrangeStack - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
- ArrangeStackBean - Class in org.anchoranalysis.image.bean.spatial.arrange
-
- ArrangeStackBean() - Constructor for class ArrangeStackBean
-
- ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
- ArrangeStackException(String) - Constructor for exception ArrangeStackException
-
- ArrangeStackException(Exception) - Constructor for exception ArrangeStackException
-
- array() - Method in class UnsignedByteBuffer
-
- array() - Method in class UnsignedIntBuffer
-
- array() - Method in class UnsignedShortBuffer
-
- as(boolean) - Static method in enum OutsideKernelPolicy
-
- asArray() - Static method in class RGBChannelNames
-
Creates an array with all channel-names in R-G-B order.
- asByte() - Method in class VoxelsWrapper
-
- asByte(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
- asByteOrCreateEmpty(boolean) - Method in class VoxelsWrapper
-
Reuses the existing buffer if byte, otherwise creates a new empty byte buffer
- asCollection() - Method in class StackSeries
-
- AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsCollection() - Constructor for class AsCollection
-
- asCollectionOrderNotPreserved() - Method in class ScaledElements
-
Returns the scaled-elements as a collection but without preserving the original element
order.
- asExtent() - Method in class SizeXY
-
Creates an extent with identical width and height and depth (z-extent) of 1
- asExtent(int) - Method in class SizeXY
-
Creates an extent with identical width and height and a specific depth (z-extent)
- asFile() - Method in interface InputFromManager
-
Expresses the input as a file with a name (the unique identifier).
- asFloat() - Method in class VoxelsWrapper
-
- asGraph() - Method in class IntersectingObjects
-
Constructs a graph where each vertex is an element and an edge exists between any elements
that intersect.
- asInt() - Method in class VoxelsWrapper
-
- asList() - Method in class FeatureList
-
- asList() - Method in class FeatureNameList
-
- asList() - Static method in class RGBChannelNames
-
Creates a list with all channel-names in R-G-B order.
- asList() - Method in class ObjectCollection
-
Exposes the underlying objects as a list
- asList() - Method in class OverlayCollection
-
- asList() - Method in class SegmentedObjects
-
Create a
List of
all contained objects,
including confidence.
- asListChannels() - Method in class Stack
-
- asListOrderPreserved(List<T>) - Method in class ScaledElements
-
Returns a list of scaled-elements corresponding to a list of unscaled-elements
- asMap() - Method in class MapCreate
-
- AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- AsMark() - Constructor for class AsMark
-
- asMarks() - Method in class EnergyMemoList
-
- AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- AsObject() - Constructor for class AsObject
-
- AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask
feature
- AsObjectMask() - Constructor for class AsObjectMask
-
- asObjects() - Method in class SegmentedObjects
-
- asOperationFailedException() - Method in exception GetOperationFailedException
-
- asOrderedArray() - Method in class Extent
-
- asPath() - Method in class RootPath
-
- asPath(boolean) - Method in class DirectoryWithPrefix
-
A path that combines the directory and fileNamePrefix and delimiter.
- asPoint() - Method in class Padding
-
- asScaleFactor() - Method in class ScaleFactorInt
-
Converts to a
ScaleFactor that accepts floating-point values.
- assertCalc(ResultsVector, Object...) - Static method in class ResultsVectorTestUtilities
-
- assertDoubleResult(String, Feature<T>, T, double) - Static method in class FeatureTestCalculator
-
- assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class FeatureTestCalculator
-
- assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class FeatureTestCalculatorDuo
-
- assertIntResult(String, Feature<T>, T, int) - Static method in class FeatureTestCalculator
-
- assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class FeatureTestCalculator
-
- assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class FeatureTestCalculatorDuo
-
- assertValid() - Method in class MarksWithEnergyBreakdown
-
- assertValid() - Method in class EnergySavedInd
-
- assertValid() - Method in class EnergySavedPairs
-
- asSet() - Static method in class RGBChannelNames
-
Creates a set of the channel names.
- asSet(Progress) - Method in interface ProvidesStackInput
-
Exposes the input as a set of named stacks (inferring the names)
- asSet() - Method in class RTree
-
All elements contained within the tree, as a
Set.
- asShort() - Method in class VoxelsWrapper
-
- asShort(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor to VoxelBuffer<UnsignedShortBuffer>
- assignAccepted(DualMarks) - Method in class DualMarksAnnotation
-
Assigns marks with an overall accepted state.
- assignBestFromCurrent() - Method in class DualState
-
- assignBoundingBox(BoundingBox) - Method in class BoundedList
-
Assigns a new containing bounding-box.
- assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class BoundedList
-
Assigns a new containing bounding-box and maps each individual element.
- assignCopyNonInputs() - Method in class InputArguments
-
- assignCurrent(Optional<T>) - Method in class DualState
-
- assignDescription(ManifestDirectoryDescription) - Method in class MutableDirectory
-
Assigns a description, which may not already exist.
- assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class IterateVoxelsAll
-
Assigns a value to any voxel whose intensity matches a predicate, reading and writing the
buffer as an int.
- assignFilterExtensions(Set<String>) - Method in class InputArguments
-
- assignFilterExtensionsIfMissing(Optional<Set<String>>) - Method in class InputArguments
-
- assignFilterGlob(String) - Method in class InputArguments
-
- assignFrom(CachedSupplierBase<T>) - Method in class CachedSupplierBase
-
- assignFrom(Mark) - Method in class VoxelizedMarkMemo
-
Assigns a new mark to replace the existing mark.
- AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Copies the pixels from channelAssignFrom to channel (possibly masking)
- AssignFromChannel() - Constructor for class AssignFromChannel
-
- AssignFromDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
- AssignFromDictionary() - Constructor for class AssignFromDictionary
-
- AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Matches source-objects to target objects, based upon intersection, and assigns the value in the
respective source object to the target object
- AssignFromIntersectingObjects() - Constructor for class AssignFromIntersectingObjects
-
- assignFunction(String) - Method in class ManifestDescription
-
Assigns a new function.
- assignIdentifierSubrange(IndexRange) - Method in class InputArguments
-
If defined, this indicates and specifies only a subset of the elements of the identifier to
use.
- assignInputDirectory(Optional<Path>) - Method in class InputArguments
-
Sets an input-directory.
- assignLogger(Logger) - Method in class OutputterChecked
-
Assigns a logger to the outputter, which is used to output warnings or messages when
outputting.
- assignMaximumIndex(int) - Method in class IncreasingIntegers
-
- assignMaximumIndex(int) - Method in class IncrementingIntegers
-
- assignMaximumIndex(int) - Method in class SequenceType
-
If the sequence-type supports a different maximum-index to that derived from the elements
SequenceType.update(T), this assigns it.
- assignMaximumIndex(int) - Method in class StringsWithoutOrder
-
- assignMaxNumberProcessors(String) - Method in class TaskArguments
-
- Assignment - Interface in org.anchoranalysis.annotation.io.assignment
-
- AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator
-
Outputs a raster showing an
Assignment on a background.
- AssignmentGenerator(DisplayStack, IntFunction<ColorPool>, boolean, Tuple2<String, String>, boolean, int) - Constructor for class AssignmentGenerator
-
- AssignmentMaskIntersection - Class in org.anchoranalysis.annotation.io.assignment
-
Calculates statistics (DICE, Jaccard etc.) based upon corresponding two object-masks
- AssignmentMaskIntersection(ObjectMask, ObjectMask) - Constructor for class AssignmentMaskIntersection
-
- AssignmentObjectFactory - Class in org.anchoranalysis.annotation.io.assignment
-
- AssignmentObjectFactory(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class AssignmentObjectFactory
-
- AssignmentOverlapFromPairs - Class in org.anchoranalysis.annotation.io.assignment
-
Pairs objects in left with objects in right
- AssignmentOverlapFromPairs() - Constructor for class AssignmentOverlapFromPairs
-
- AssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
How assignments and other decisions are made in the SimulatedAnnealing optimizaton
- AssignMode() - Constructor for class AssignMode
-
- assignModelDirectory(Path) - Method in class InputArguments
-
- assignOff() - Method in class Mask
-
- assignOff() - Method in class BinaryVoxels
-
- assignOff() - Method in class ObjectMask
-
Assigns OFF value to voxels, expecting global coordinates
- assignOn() - Method in class Mask
-
- assignOn() - Method in class BinaryVoxels
-
- assignOn() - Method in class ObjectMask
-
Assigns ON value to voxels, expecting global coordinates
- assignOutputDirectory(Path) - Method in class OutputPrefixerSettings
-
- assignParentDirectory(Optional<MutableDirectory>) - Method in class MutableDirectory
-
- assignPath(Path) - Method in class SubdirectoryBase
-
- assignPaths(List<Path>) - Method in class InputArguments
-
- assignPaused(DualMarks) - Method in class DualMarksAnnotation
-
Assigns marks with an overall paused state.
- assignPrevious(double, int) - Method in class UnchangedBase
-
Assigns the previous value to be remembered for comparison next time.
- assignPrevious(double, int) - Method in class UnchangedScore
-
- assignPrevious(double, int) - Method in class UnchangedSize
-
- AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
- AssignPriority() - Constructor for class AssignPriority
-
- assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class AssignPriority
-
Assigns a priority to a potential merge
- AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Allows merges if there is an increase in the payload i.e.
- AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class AssignPriorityFromImprovement
-
- AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Calculates pair-feature on each potential merge, and this value determines priority..
- AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, RelationToValue) - Constructor for class AssignPriorityFromPair
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriority
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromImprovement
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromPair
-
- assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in interface KernelAssigner
-
- assignProposal(Optional<T>, KernelWithIdentifier<S, V>) - Method in class OptimizationStep
-
- assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in class KernelAssignerAddErrorLevel
-
- assignProposal(OptimizationStep<S, T, V>, TransformationContext, KernelWithIdentifier<S, V>) - Method in class KernelAssignerCalculateEnergyFromKernel
-
- assignRejected(DualMarks, T) - Method in class DualMarksAnnotation
-
Assigns marks with an overall rejected state.
- assignRelativeForIdentifier() - Method in class InputArguments
-
- assignShuffle() - Method in class InputArguments
-
- assignSize(String) - Method in class TaskArguments
-
- assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputArguments
-
- assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputPrefixerSettings
-
- assignTaskName(Optional<String>) - Method in class TaskArguments
-
- assignType(String) - Method in class ManifestDescription
-
Assigns a new type.
- assignValue(int) - Method in class Channel
-
- assignValue(int) - Method in class BoundedVoxels
-
Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes
etc.
- assignValue(int) - Method in class Voxels
-
Provides a means to assign a constant-value to some or all of the voxels.
- assignValue(int) - Method in class VoxelsAsFloat
-
- assignValue(int) - Method in class VoxelsAsInt
-
- assignValue(int) - Method in class VoxelsAsShort
-
- assignValue(int) - Method in class VoxelsUnsignedByte
-
- assignValue(int) - Method in class VoxelsWrapper
-
- AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Assigns a constant (scalar) value to the portion of the image covered by a mask
- AssignValue() - Constructor for class AssignValue
-
- AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element
-
- AsSingle() - Constructor for class AsSingle
-
- AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsSingleMark() - Constructor for class AsSingleMark
-
- associated - Variable in class AddOptionsFromCommandLine
-
An associated entity which consumers accept.
- associatedFile() - Method in class AnnotationWithStrategy
-
- associateXml(XMLConfiguration) - Method in interface AssociateXmlUponLoad
-
Associated
- associateXml(XMLConfiguration) - Method in class Experiment
-
- associateXml(XMLConfiguration) - Method in class QuickMultiDatasetStructuredExperiment
-
- AssociateXmlUponLoad - Interface in org.anchoranalysis.bean.xml
-
For classes that wish to have a XmlConfiguration associated with them
- asStack() - Method in class EnergyStack
-
- asStack() - Method in class EnergyStackWithoutParams
-
- asStack() - Method in class RGBStack
-
- asTuple() - Method in class Extent
-
Exposes the extent as a tuple.
- at(int, int, int, int) - Static method in class BoundingBoxFactory
-
Short-hand factory method for creating a 2D bounding-box.
- at(int, int, int, int, int, int) - Static method in class BoundingBoxFactory
-
Short-hand factory method for creating a 3D bounding-box.
- atanHandlingNan(double) - Static method in class EllipseStandardFormConverter
-
- atBorder(Extent) - Method in class BoundingBox
-
- AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderBase() - Constructor for class AtBorderBase
-
- AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderXY() - Constructor for class AtBorderXY
-
- atBorderXY(Extent) - Method in class BoundingBox
-
- AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderZ() - Constructor for class AtBorderZ
-
- atBorderZ(Extent) - Method in class BoundingBox
-
- atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class VoxelsExtracterFactory
-
- AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Creates a new object-collection with only a single element (at a particular index) in the
existing collection.
- AtIndex() - Constructor for class AtIndex
-
- AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.file.group.check
-
- AtLeastZSlices() - Constructor for class AtLeastZSlices
-
- AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Perform a segmentation at a different scale, and then fit the results back to the original scale.
- AtScale() - Constructor for class AtScale
-
- attachObject(Channel) - Method in class MaxIntensity
-
- attachObject(S) - Method in interface ChannelConverterAttached
-
- attachObject(Histogram) - Method in class MaxIntensityFromHistogram
-
- attachObject(Histogram) - Method in class QuantileIntensityFromHistogram
-
- attachObject(Histogram) - Method in class UpperLowerQuantileIntensityFromHistogram
-
- AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider
-
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
- AutoLocalThreshold() - Constructor for class AutoLocalThreshold
-
- Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
Names of the channels from the metadata if it exists, or after RGB, or by index
- Autoname() - Constructor for class Autoname
-
- AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
-
- AxisAlignedUnitVector() - Constructor for class AxisAlignedUnitVector
-
- AxisLimits - Class in org.anchoranalysis.plot
-
- AxisLimits() - Constructor for class AxisLimits
-
- AxisLimits(double, double) - Constructor for class AxisLimits
-
- AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature
-
- AxisRatioEllipsoid() - Constructor for class AxisRatioEllipsoid
-
- AxisType - Enum in org.anchoranalysis.spatial.axis
-
- AxisTypeConverter - Class in org.anchoranalysis.spatial.axis
-
Converts to/from
AxisType to string representations and integer index (0 for X, 1 for Y,
2 for Z)
- AxisTypeException - Exception in org.anchoranalysis.spatial.axis
-
- AxisTypeException(String) - Constructor for exception AxisTypeException
-
- cache(CheckedSupplier<T, E>) - Static method in class CachedSupplier
-
- cache(StoreSupplier<T>) - Static method in interface StoreSupplier
-
Memoizes (caches) the supplied object, and returning it with an identical interface
- cache(CheckedProgressingSupplier<T, E>) - Static method in class CachedProgressingSupplier
-
- cache(NamedStacksSupplier) - Static method in interface NamedStacksSupplier
-
- cache(SerializedObjectSupplier<T>) - Static method in interface SerializedObjectSupplier
-
- CACHE_NAME_FIRST - Static variable in class FeatureDeriveFromPair
-
- CACHE_NAME_MERGED - Static variable in class FeatureDeriveFromPair
-
- CACHE_NAME_SECOND - Static variable in class FeatureDeriveFromPair
-
- CacheAndReuseStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace
-
Reuse (without needing to invalidate) an existing session-input as stored in a least-recently
used cache, otherwise create a new one.
- CacheAndReuseStrategy(CacheCreator) - Constructor for class CacheAndReuseStrategy
-
- CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache
-
- CachedProgressingSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.progress
-
- CachedSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.cache
-
- CachedSupplierBase<T> - Class in org.anchoranalysis.core.cache
-
Base class for functions that memoize (cache) a call to an interface
- CachedSupplierBase() - Constructor for class CachedSupplierBase
-
- cacheName() - Method in class DerivedObject
-
- cacheName() - Method in class Erode
-
- cacheName() - Method in class Shell
-
- cacheResettable(StoreSupplier<T>) - Static method in interface StoreSupplier
-
Memoizes (caches) the supplied object, and returning it with a
CachedSupplier
interface
- cachesToAvoidInvalidating() - Method in class CheckCacheForSpecificChildren
-
- cachesToAvoidInvalidating() - Method in interface ChildCacheFinder
-
If set, these particular-caches are exceptionall NOT invalidated during the typical
invalidation operation on their parent.
- cachesToAvoidInvalidating() - Method in class DefaultChildCacheFinder
-
- CacheSupplier<T extends FeatureInput,E extends Exception> - Interface in org.anchoranalysis.feature.session.cache.finder
-
- CacheTransferSource<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.finder
-
An existing cache that can be used as a source for child-caches elsewhere.
- CacheTransferSource(CacheSupplier<T, OperationFailedException>, Set<ChildCacheName>) - Constructor for class CacheTransferSource
-
- CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.cache.finder
-
- CacheTransferSourceCollection() - Constructor for class CacheTransferSourceCollection
-
- calc(FeatureList<T>, SessionInput<T>) - Method in interface FeatureSessionCalculator
-
Calculates a feature-list throwing an exception if there is an error
- calc(FeatureInputObjectCollection) - Method in class FeatureObjectCollection
-
- calc(FeatureInputMarkCollection) - Method in class FeatureMarkCollection
-
- calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParams) - Method in class EnergySavedAll
-
- calc(FeatureInputObjectCollection) - Method in class NumberObjects
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class MaskAsSingleObject
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class ObjectAggregationBase
-
- calc(SessionInput<T>, FeatureCalculation<U, T>, Function<ResolvedCalculation<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class CalculateInputFromDelegateOption
-
Calculates a feature using a cached-calculation as delegate, and optional Params return value
- calc(FeatureInputMarkCollection) - Method in class NumberMarks
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class AxisRatioEllipsoid
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class EllipsoidBase
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class Ellipsoidicity
-
- calculate(SessionInput<T>) - Method in class Feature
-
- calculate(SessionInput<T>) - Method in class Constant
-
- calculate(SessionInput<T>) - Method in class Reference
-
- calculate(SessionInput<T>) - Method in class Sum
-
- calculate(FeatureInputResults) - Method in class Count
-
- calculate(SessionInput<FeatureInputResults>) - Method in class FeatureResults
-
- calculate(FeatureInputResults) - Method in class FeatureResults
-
- calculate(FeatureInputResults) - Method in class StatisticForFeature
-
- calculate(Feature<S>, S, ChildCacheName) - Method in interface CalculateForChild
-
Calculates a feature in a child-cache
- calculate(Feature<S>, FeatureCalculation<S, T>, ChildCacheName) - Method in interface CalculateForChild
-
- calculate(ChildCacheName, S, Function<CalculationResolver<S>, ResolvedCalculation<U, S>>) - Method in interface CalculateForChild
-
- calculate(Feature<T>, SessionInput<T>) - Method in interface FeatureSessionCalculator
-
Calculate a feature with particular values
- calculate(Feature<T>) - Method in interface SessionInput
-
Calculates the result of a feature using this input
- calculate(FeatureList<T>) - Method in interface SessionInput
-
Calculates the results of several features using this input
- calculate(FeatureCalculation<S, T>) - Method in interface SessionInput
-
Calculates a feature-calculation after resolving it against the main cache
- calculate(ResolvedCalculation<S, T>) - Method in interface SessionInput
-
Calculates a resolved Feature-calculation
- calculate(T) - Method in class FeatureCalculatorCachedMulti
-
- calculate(T, FeatureList<T>) - Method in class FeatureCalculatorCachedMulti
-
- calculate(T) - Method in interface FeatureCalculatorMulti
-
Performs one calculation throwing an exception if something goes wrong
- calculate(T, FeatureList<T>) - Method in interface FeatureCalculatorMulti
-
Performs one calculation on a sub-set of the feature list throwing an exception if something
goes wrong
- calculate(T, ErrorReporter, boolean) - Method in interface FeatureCalculatorMulti
-
- calculate(T) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T, FeatureList<T>) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T) - Method in class FeatureCalculatorCachedSingle
-
- calculate(T) - Method in interface FeatureCalculatorSingle
-
Performs one calculation throwing an exception if something goes wrong
- calculate(T) - Method in class FeatureCalculatorSingleChangeInput
-
- calculate(T) - Method in class FeatureCalculatorSingleFromMulti
-
- calculate(T) - Method in class SequentialSession
-
Calculates one params for each feature.
- calculate(T, FeatureList<T>) - Method in class SequentialSession
-
- calculate(Feature<T>) - Method in class SessionInputSequential
-
- calculate(FeatureList<T>) - Method in class SessionInputSequential
-
- calculate(FeatureCalculation<S, T>) - Method in class SessionInputSequential
-
- calculate(ResolvedCalculation<S, T>) - Method in class SessionInputSequential
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ScaleCalculator
-
Calculates a scaling-factor for a source image/entity of particular dimensions.
- calculate(SessionInput<FeatureInputHistogram>) - Method in class FeatureHistogramStatistic
-
- calculate(SessionInput<FeatureInputObjectCollection>) - Method in class FeatureObjectCollection
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class First
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Merged
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Minimum
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class RatioFirstToSecond
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Second
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class SubtractSecondFromFirst
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class CenterOfGravity
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class NumberVoxels
-
- calculate(SessionInput<T>) - Method in class WithResolutionBase
-
- calculate(int[]) - Method in class VoxelScore
-
- calculate(FeatureInputPairObjects) - Method in class PairsTableCalculator
-
- calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class PairsTableCalculator
-
- calculate(FeatureInputSingleObject) - Method in class SingleTableCalculator
-
- calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class SingleTableCalculator
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class AsSingle
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class FeatureSingleMemo
-
- calculate(SessionInput<FeatureInputMarkCollection>) - Method in class FeatureMarkCollection
-
- calculate(SessionInput<FeatureInputMark>) - Method in class FeatureMark
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ConstantScaleFactor
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class Invert
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class LargestMultipleWithin
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class MinimumXYResolution
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToDimensions
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToSuggested
-
- calculate(SessionInput<T>) - Method in class FromDimensionsBase
-
- calculate(SessionInput<FeatureInputHistogram>) - Method in class LevelFromHistogram
-
- calculate(SessionInput<FeatureInputHistogram>) - Method in class ThresholdHistogram
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class Intersection
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class CostOverlapWithinMidpointDistance
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class OverlapRelative
-
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class TouchingVoxels
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ArbitraryInsidePoint
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class AtBorderBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class BoundingBoxAlongAxisBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class BoundingBoxNumberVoxels
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class SpecificEnergyChannelBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class FeatureEnergyChannel
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class GradientMagnitude
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class GradientMeanForAxis
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ImageMomentsBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class DerivedObject
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class NumberRemovedVoxelsAfterClosing
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class OutlineKernelBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ObjectRadiusStandardDeviation
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ShapeRegularityCenterSlice
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class ShapeRegularityMIP
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class PairedWithMask
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class MaximumNumberContourVoxelsOnSlice
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class MaximumNumberVoxelsOnSlice
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class SurfaceNumberVoxelsBase
-
- calculate(int[]) - Method in class Difference
-
- calculate(int[]) - Method in class Identity
-
- calculate(int[]) - Method in class IdentityImposeValueRelationToHistogram
-
- calculate(int[]) - Method in class OutsideRange
-
- calculate(int[]) - Method in class RejectIfIntensityLessThan
-
- calculate(int[]) - Method in class SingleChannel
-
- calculate(SessionInput<T>) - Method in class FeatureSingleObjectFromShared
-
- calculate(SessionInput<T>) - Method in class ParamFromCollection
-
- calculate(SessionInput<T>) - Method in class DataTypeMaxIntensity
-
- calculate(SessionInput<FeatureInputStack>) - Method in class Intensity
-
- calculate(SessionInput<FeatureInputStack>) - Method in class NumberChannels
-
- calculate(SessionInput<FeatureInputStack>) - Method in class AsObjectMask
-
- calculate(SessionInput<FeatureInputStack>) - Method in class QuantileAcrossConnectedComponents
-
- calculate(ObjectMask) - Method in interface PayloadCalculator
-
- calculate(SessionInput<FeatureInputMark>) - Method in class FeatureMarkDirection
-
- calculate(SessionInput<FeatureInputMark>) - Method in class FeatureMarkEccentricity
-
- calculate(SessionInput<FeatureInputMark>) - Method in class MaxRatioRadii
-
- calculate(SessionInput<FeatureInputMark>) - Method in class OrderedRadius
-
- calculate(SessionInput<FeatureInputMark>) - Method in class RadiiRatio
-
- calculate(SessionInput<FeatureInputMark>) - Method in class BoundingBoxExtent
-
- calculate(SessionInput<FeatureInputMark>) - Method in class MarkEllipseCircumEstimate
-
- calculate(SessionInput<FeatureInputMark>) - Method in class Volume
-
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class AsCollection
-
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class AsSingleMark
-
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class CoefficientOfVarianceFromAll
-
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class MeanFromAll
-
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class NumberMarks
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class AsMark
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class AsObject
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class BBoxRatio
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class Intensity
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class MaxSliceArea
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class MeanIntensityDifference
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class Size
-
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class SurfaceSizeMaskNonZero
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class BoundingBoxZDistance
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class BoundingBoxZOverlapRatio
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class MinimumDistanceByDimension
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class FeatureAsIndividualProportionate
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class MinFeatureAsIndividual
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class MaxOverlapRatio
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxels
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxelsMask
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapRatio
-
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class OverlapRatioMask
-
- calculate(SessionInput<FeatureInputStack>) - Method in class HOGFeature
-
- calculate(SessionInput<T>) - Method in class AbsoluteValue
-
- calculate(SessionInput<T>) - Method in class Divide
-
- calculate(SessionInput<T>) - Method in class InvertedMax
-
- calculate(SessionInput<T>) - Method in class Multiply
-
- calculate(SessionInput<T>) - Method in class IfCondition
-
- calculate(SessionInput<T>) - Method in class FromDictionary
-
- calculate(SessionInput<T>) - Method in class Maximum
-
- calculate(SessionInput<T>) - Method in class Mean
-
- calculate(SessionInput<T>) - Method in class MeanGeometric
-
- calculate(SessionInput<T>) - Method in class Minimum
-
- calculate(SessionInput<T>) - Method in class NormalizedRange
-
- calculate(SessionInput<T>) - Method in class Range
-
- calculate(SessionInput<T>) - Method in class RangeCompareBase
-
- calculate(SessionInput<T>) - Method in class StatisticalBase
-
- calculate(SessionInput<T>) - Method in class WithValueBase
-
- calculate(SessionInput<T>) - Method in class ConvertUnits
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class EllipsoidBase
-
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class Ellipticity
-
- calculate(SessionInput<FeatureInput>) - Method in class MockFeatureWithCalculation
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class Kernel
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirth
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirthAndKill
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelDeath
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelExchange
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksFromPartition
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksProposed
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksVoxelized
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelMerge
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelReplace
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelSplit
-
- calculateAcceptanceProbability(Kernel<?, ?>, Optional<T>, T, int, KernelCalculationContext) - Method in class AcceptanceProbabilityCalculator
-
- calculateAt(KernelPointCursor) - Method in class AndKernel
-
- calculateAt(KernelPointCursor) - Method in class BinaryKernel
-
Calculates the boolean at a particular point.
- calculateAt(KernelPointCursor) - Method in class ConditionalKernel
-
- calculateAt(KernelPointCursor) - Method in class CountKernel
-
Calculates the count at a particular point.
- calculateAt(KernelPointCursor) - Method in class BinaryKernelMorphological
-
- calculateBytesPerPixel(int) - Method in class ToUnsignedByte
-
- calculateBytesPerPixel(int) - Method in class UnsignedByteFromFloat
-
- calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedByteInterleaving
-
- calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
-
- calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedInt
-
- calculateBytesPerPixel(int) - Method in class UnsignedByteFromUnsignedShort
-
- calculateCheckInitialized(SessionInput<T>) - Method in class Feature
-
- calculateConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
-
- calculateContext(MarkFactoryContext) - Method in class OptimizationContext
-
- calculateCornerMax() - Method in class BoundingBox
-
The maximum (right-most) point inside the box.
- calculateCornerMaxExclusive() - Method in class BoundingBox
-
The maximum (right-most) point just outside the box.
- calculateCountNonZero() - Method in class Histogram
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelative
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToFirst
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMaxVolume
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMerged
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToSecond
-
- calculateDensityRatio(double, double, int) - Method in class AnnealScheme
-
- CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CalculateDeriveMarkCollectionInput() - Constructor for class CalculateDeriveMarkCollectionInput
-
- CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CalculateDeriveMarkInput() - Constructor for class CalculateDeriveMarkInput
-
- CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
- CalculateDeriveObjectInput(int) - Constructor for class CalculateDeriveObjectInput
-
- CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
-
- CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class CalculateDeriveSingleMemoFromPair
-
- CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateDilationMap(boolean) - Constructor for class CalculateDilationMap
-
- CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateDilationMap
-
- calculateEccentricity(double, double) - Static method in class PrincipalAxisEccentricity
-
- CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
-
- CalculateEllipseLeastSquares() - Constructor for class CalculateEllipseLeastSquares
-
- CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
-
- CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateErosionMap(boolean) - Constructor for class CalculateErosionMap
-
- CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class CalculateErosionMap
-
- calculateFeatureByIdentifier(String, SessionInput<T>) - Method in interface FeatureSymbolCalculator
-
Searches for a feature that matches a particular identifier
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class ReportFeatureOnObject
-
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class ReportFeatureOnObjectCollection
-
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class ReportFeatureOnObjectsBase
-
- CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
-
- CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitializationWithEnergyStack, boolean, InputProcessContext<FeatureTableCalculator<T>>) - Constructor for class CalculateFeaturesForObjects
-
- calculateFeaturesForObjects(ObjectCollection, EnergyStack, CalculateFeaturesForObjects.LabelsForInput<T>) - Method in class CalculateFeaturesForObjects
-
- CalculateFeaturesForObjects.LabelsForInput<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.task.feature.calculator
-
- calculateForAxis(Dimensions, AxisType) - Method in class Extent
-
- calculateForAxis(Dimensions, AxisType) - Method in class ForSpecificAxis
-
- calculateForAxis(Dimensions, AxisType) - Method in class VoxelPhysicalSize
-
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class FeatureEnergyChannel
-
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class Intensity
-
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanMaxSlice
-
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanShellBase
-
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class TextureScore
-
- CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Performs calculations using child-caches instead of the main cache
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class DotProductOrientationToVector
-
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class EllipsoidAxisRatio
-
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class EllipsoidMaxAreaIntersectingPlane
-
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class FeatureMarkDirection
-
- calculateForNewMark(MarksFromPartition, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthPartition
-
- calculateForNewMark(T, Set<Mark>, KernelCalculationContext) - Method in class KernelBirth
-
- calculateForNewMark(VoxelizedMarksWithEnergy, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthPixelized
-
- calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShell
-
- calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellBase
-
- calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellMaxSlice
-
- calculateForVoxel(int, int) - Method in class CalculateLevel
-
- calculateForVoxel(int, int) - Method in class CalculateLevelBase
-
- calculateForVoxel(int, int) - Method in class DifferenceCalculateLevelStandardDeviation
-
- calculateFromAllMoments(ImageMoments) - Method in class ImageMomentsBase
-
- calculateFromAllMoments(ImageMoments) - Method in class PrincipalAxisEccentricity
-
- calculateFromAllMoments(ImageMoments) - Method in class RatioPrincipalAxisLength
-
- calculateFromAllMoments(ImageMoments) - Method in class SpecificAxisBase
-
- calculateFromDimensions(Dimensions) - Method in class Area
-
- calculateFromDimensions(Dimensions) - Method in class ForSpecificAxis
-
- calculateFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- calculateFromDimensions(Dimensions) - Method in class Volume
-
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisLength
-
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisOrientation
-
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class SpecificAxisBase
-
Calculates the result for the specific moment identified by index
- CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
-
- CalculateHistogram(int) - Constructor for class CalculateHistogram
-
- CalculateHistogramMasked - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
-
Calculated a histogram for a specific region on a channel, as identified by a mask in another
channel
- CalculateHistogramMasked(int, int) - Constructor for class CalculateHistogramMasked
-
- CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateIncrementalOperationMap(boolean) - Constructor for class CalculateIncrementalOperationMap
-
- CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateIncrementalOperationMap
-
- CalculateInputFromDelegate<S,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
A base class for Cached-Calculations that generate a Params for feature-calculation using an
existing "delegate" calculation
- CalculateInputFromDelegate(FeatureCalculation<U, T>, CalculationResolver<T>) - Constructor for class CalculateInputFromDelegate
-
- CalculateInputFromDelegate(ResolvedCalculation<U, T>) - Constructor for class CalculateInputFromDelegate
-
- CalculateInputFromDelegateOption<S extends FeatureInput,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
- CalculateInputFromDelegateOption(ResolvedCalculation<U, T>) - Constructor for class CalculateInputFromDelegateOption
-
The constructor
- CalculateInputFromPair - Class in org.anchoranalysis.image.feature.calculation
-
Calculates a single-input from a pair
- CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class CalculateInputFromPair
-
- CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.calculation
-
- CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
- CalculateIntersecting(ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class CalculateIntersecting
-
- CalculateLevel - Class in org.anchoranalysis.image.bean.threshold
-
Calculates a threshold-level from a histogram.
- CalculateLevel() - Constructor for class CalculateLevel
-
- calculateLevel(Histogram) - Method in class CalculateLevel
-
Determines a voxel intensity that can be used for thresholding.
- calculateLevel(Histogram) - Method in class CalculateLevelRelativeToThreshold
-
- calculateLevel(Histogram) - Method in class ClampHistogramMax
-
- calculateLevel(Histogram) - Method in class Constant
-
- calculateLevel(Histogram) - Method in class EmptyHistogramConstant
-
- calculateLevel(Histogram) - Method in class Maximum
-
- calculateLevel(Histogram) - Method in class Minimum
-
- calculateLevel(Histogram) - Method in class Otsu
-
- calculateLevel(Histogram) - Method in class OtsuWeighted
-
- calculateLevel(Histogram) - Method in class Quantile
-
- CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- CalculateLevel() - Constructor for class CalculateLevel
-
- CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- CalculateLevelBase() - Constructor for class CalculateLevelBase
-
- calculateLevelIncoming(Histogram) - Method in class CalculateLevelOne
-
- CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
- CalculateLevelListBase() - Constructor for class CalculateLevelListBase
-
- CalculateLevelOne - Class in org.anchoranalysis.image.bean.threshold
-
- CalculateLevelOne() - Constructor for class CalculateLevelOne
-
- CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
- CalculateLevelRelativeToThreshold() - Constructor for class CalculateLevelRelativeToThreshold
-
- calculateMaximum() - Method in class Histogram
-
Calculates the maximum of the histogram values i.e.
- calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
-
- calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class IntensityMeanCalculator
-
- calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class IntensityMeanCalculator
-
- calculateMemoryUsage() - Static method in class MemoryUtilities
-
- calculateMidpoint(ObjectWithProperties, boolean) - Static method in class Midpoint
-
- calculateMinimum() - Method in class Histogram
-
Calculates the minimum of the histogram values i.e.
- calculateMinMax(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- calculateMode() - Method in class Histogram
-
- calculateMode(int) - Method in class Histogram
-
Calculates the mode of the histogram values i.e.
- calculateNewMaxCurrentValue() - Method in class PriorityQueueIndexRangeDownhill
-
- CalculateNumberVoxels - Class in org.anchoranalysis.image.feature.calculation
-
- CalculateNumberVoxels(boolean) - Constructor for class CalculateNumberVoxels
-
- CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateObjectMask(CalculateObjectMask) - Constructor for class CalculateObjectMask
-
Copy constructor
- CalculateObjectMask(int, ResolvedCalculationMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class CalculateObjectMask
-
- calculateOrientation(ObjectWithProperties) - Static method in class Orientation
-
- CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlap(int) - Constructor for class CalculateOverlap
-
- CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMask(int, int, byte) - Constructor for class CalculateOverlapMask
-
- CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIP(int) - Constructor for class CalculateOverlapMIP
-
- CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIPBase(int) - Constructor for class CalculateOverlapMIPBase
-
- CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIPRatio(int) - Constructor for class CalculateOverlapMIPRatio
-
- calculateOverlapRatio(ObjectMask, ObjectMask, ObjectMask) - Static method in class OverlapCalculator
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIP
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPBase
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPRatio
-
- calculatePath() - Method in class MutableDirectory
-
- calculatePath() - Method in class OutputtedFile
-
- calculatePoint(ObjectWithProperties, String) - Static method in class Orientation
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class MergeLists
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class PointsFromOrientationProposer
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class TraversePointsOnContour
-
- calculateResultsForInput(FileInput, InputProcessContext<FeatureList<FeatureInputHistogram>>) - Method in class FromHistogram
-
- calculateResultsForInput(ProvidesStackInput, InputProcessContext<FeatureList<FeatureInputStack>>) - Method in class FromImage
-
- calculateResultsForInput(T, InputProcessContext<FeatureList<S>>) - Method in class SingleRowPerInput
-
- calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class IterateVoxelsMask
-
Calculates the sum and count across voxels intensity that correspond to on voxels on a
mask
- calculateScaleFactor(Optional<Dimensions>) - Method in interface ImageSizeSuggestion
-
Calculates the scaling factor.
- CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateShellObjectMask(ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class CalculateShellObjectMask
-
- calculateSigma(Dimensions, MessageLogger) - Method in class BlurStrategy
-
- calculateStatisticFrom(Histogram) - Method in class FeatureHistogramStatistic
-
- calculateStatisticFrom(Histogram) - Method in class Mean
-
- calculateStatisticFrom(Histogram) - Method in class CoefficientOfVariation
-
- calculateStatisticFrom(Histogram) - Method in class Count
-
- calculateStatisticFrom(Histogram) - Method in class Kurtosis
-
- calculateStatisticFrom(Histogram) - Method in class Max
-
- calculateStatisticFrom(Histogram) - Method in class MeanRaisedToPower
-
- calculateStatisticFrom(Histogram) - Method in class Median
-
- calculateStatisticFrom(Histogram) - Method in class Min
-
- calculateStatisticFrom(Histogram) - Method in class Mode
-
- calculateStatisticFrom(Histogram) - Method in class NumberDistinctValues
-
- calculateStatisticFrom(Histogram) - Method in class Quantile
-
- calculateStatisticFrom(Histogram) - Method in class Range
-
- calculateStatisticFrom(Histogram) - Method in class RatioNonMode
-
- calculateStatisticFrom(Histogram) - Method in class Skewness
-
- calculateStatisticFrom(Histogram) - Method in class StdDev
-
- calculateStatisticFrom(Histogram) - Method in class Sum
-
- calculateStatisticFrom(Histogram) - Method in class TotalCount
-
- calculateStatisticFrom(Histogram) - Method in class Variance
-
- calculateStatisticFrom(Histogram) - Method in class RatioThreshold
-
- calculateSum() - Method in class Histogram
-
- calculateSumCubes() - Method in class Histogram
-
- calculateSumSquares() - Method in class Histogram
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorCachedMulti
-
- calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorMulti
-
Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but
throwing no exception
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorMultiChangeInput
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorCachedSingle
-
- calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorSingle
-
Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but
throwing no exception
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleChangeInput
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleFromMulti
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class SequentialSession
-
Calculates the next-object in our sequential series, reporting any exceptions into a reporter
log
- calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
-
- calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class SingleTableCalculator
-
- calculateTemperature(int) - Method in class AnnealScheme
-
- calculateTemperature(int) - Method in class Geometry
-
- calculateTemperature(int) - Method in class NoAnnealing
-
- calculateVolume() - Method in class Dimensions
-
- calculateVolume() - Method in class Extent
-
- calculateVolumeAsInt() - Method in class Extent
-
- calculateWith(Feature<T>, T, Logger) - Static method in class FeatureSession
-
Starts a feature-session for a single feature - and performs a calculation
- calculateWithChannel(ObjectMask, Channel) - Method in class CountEqual
-
- calculateWithChannel(ObjectMask, Channel) - Method in class SpecificEnergyChannelBase
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class HasTouchingVoxels
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxelFaces
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxels
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class TouchingVoxels
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberVoxelsAtBorder
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberNeighboringVoxels
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class OutlineKernelBase
-
- calculateWithResolution(double, Resolution) - Method in class FeatureConvertUnits
-
- calculateWithResolution(double, Resolution) - Method in class WithResolutionBase
-
- calculateWithResolution(double, Resolution) - Method in class UnitsWithinRange
-
- calculateZScore(double, double, double) - Static method in class FirstSecondOrderStatistic
-
- CalculationResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
- calculator() - Method in interface FeatureSessionCache
-
A means of calculating feature values using this cache.
- calculatorForAll(FeatureList<T>) - Method in class FeatureCalculatorFromProvider
-
Calculates all image-features in the feature-store
- calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class FeatureCalculatorFromProvider
-
Calculates a single-feature that comes from a provider (but can reference the other features
from the store)
- call(CheckedSupplier<T, E>) - Method in class CachedSupplierBase
-
- call() - Method in class CallableJob
-
- CallableJob<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.task.processor
-
A job derived from a
Task that can be placed on different threads
- CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobState, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class CallableJob
-
Constructor
- callChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class ChannelMapper
-
- callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class IterateVoxelsNeighbors
-
Iterate over each point in the neighborhood of an existing point.
- canEqual(Object) - Method in class RootPath
-
- canEqual(Object) - Method in class EqualToBean
-
- canEqual(Object) - Method in class GreaterThanBean
-
- canEqual(Object) - Method in class GreaterThanEqualToBean
-
- canEqual(Object) - Method in class LessThanBean
-
- canEqual(Object) - Method in class LessThanEqualToBean
-
- canEqual(Object) - Method in class RelationBean
-
- canEqual(Object) - Method in class RelationToConstant
-
- canEqual(Object) - Method in class WithPriority
-
- canEqual(Object) - Method in class IdentifierModulo
-
- canEqual(Object) - Method in class Indexable
-
- canEqual(Object) - Method in class ChildCacheName
-
- canEqual(Object) - Method in class FeatureInputEnergy
-
- canEqual(Object) - Method in class FeatureInputNull
-
- canEqual(Object) - Method in class SimpleName
-
- canEqual(Object) - Method in class SizeXY
-
- canEqual(Object) - Method in class CalculateLevelOne
-
- canEqual(Object) - Method in class BinaryNotOffVoxels
-
- canEqual(Object) - Method in class BinaryNotOnVoxels
-
- canEqual(Object) - Method in class BinaryOffVoxels
-
- canEqual(Object) - Method in class BinaryOnVoxels
-
- canEqual(Object) - Method in class BinaryVoxelsBase
-
- canEqual(Object) - Method in class Orientation2D
-
- canEqual(Object) - Method in class Orientation3DEulerAngles
-
- canEqual(Object) - Method in class OrientationAxisAngle
-
- canEqual(Object) - Method in class OrientationIdentity
-
- canEqual(Object) - Method in class OrientationRotationMatrix
-
- canEqual(Object) - Method in class CalculateInputFromPair
-
- canEqual(Object) - Method in class CalculateNumberVoxels
-
- canEqual(Object) - Method in class FeatureInputObjectCollection
-
- canEqual(Object) - Method in class FeatureInputPairObjects
-
- canEqual(Object) - Method in class FeatureInputSingleObject
-
- canEqual(Object) - Method in class FeatureInputStack
-
- canEqual(Object) - Method in class UnsignedBuffer
-
- canEqual(Object) - Method in class UnsignedBufferAsInt
-
- canEqual(Object) - Method in class UnsignedByteBuffer
-
- canEqual(Object) - Method in class UnsignedIntBuffer
-
- canEqual(Object) - Method in class UnsignedShortBuffer
-
- canEqual(Object) - Method in class QuadraticEquationSolver.QuadraticRoots
-
- canEqual(Object) - Method in class FirstSecondOrderStatistic
-
- canEqual(Object) - Method in class RegionMap
-
- canEqual(Object) - Method in class RegionMembership
-
- canEqual(Object) - Method in class RegionMembershipWithFlags
-
- canEqual(Object) - Method in class CalculateDeriveSingleMemoFromPair
-
- canEqual(Object) - Method in class FeatureInputMark
-
- canEqual(Object) - Method in class IndexableMarksWithEnergy
-
- canEqual(Object) - Method in class FeatureInputAllMemo
-
- canEqual(Object) - Method in class FeatureInputPairMemo
-
- canEqual(Object) - Method in class FeatureInputSingleMemo
-
- canEqual(Object) - Method in class MemoList
-
- canEqual(Object) - Method in class ColoredMarksWithDisplayStack
-
- canEqual(Object) - Method in class MarksWithDisplayStack
-
- canEqual(Object) - Method in class OverlayMark
-
- canEqual(Object) - Method in class FeedbackBeginParameters
-
- canEqual(Object) - Method in class IndexableOverlays
-
- canEqual(Object) - Method in class AxisLimits
-
- canEqual(Object) - Method in class AnnotationGroup
-
- canEqual(Object) - Method in class AnnotationGroupObject
-
- canEqual(Object) - Method in class CalculateLevelListBase
-
- canEqual(Object) - Method in class CalculateLevelRelativeToThreshold
-
- canEqual(Object) - Method in class ClampHistogramMax
-
- canEqual(Object) - Method in class Constant
-
- canEqual(Object) - Method in class EmptyHistogramConstant
-
- canEqual(Object) - Method in class IfGreaterThan
-
- canEqual(Object) - Method in class IfLessThan
-
- canEqual(Object) - Method in class Maximum
-
- canEqual(Object) - Method in class Minimum
-
- canEqual(Object) - Method in class Otsu
-
- canEqual(Object) - Method in class OtsuWeighted
-
- canEqual(Object) - Method in class Quantile
-
- canEqual(Object) - Method in class MorphologicalIterations
-
- canEqual(Object) - Method in class CalculateIntersecting
-
- canEqual(Object) - Method in class CalculateDeriveObjectInput
-
- canEqual(Object) - Method in class CalculateInputFromDelegate
-
- canEqual(Object) - Method in class CalculateInputFromDelegateOption
-
- canEqual(Object) - Method in class CalculateIncrementalOperationMap
-
- canEqual(Object) - Method in class CalculateObjectMask
-
- canEqual(Object) - Method in class CalculateShellObjectMask
-
- canEqual(Object) - Method in class CalculateDilation
-
- canEqual(Object) - Method in class CalculateDilationMap
-
- canEqual(Object) - Method in class CalculateErosion
-
- canEqual(Object) - Method in class CalculateErosionMap
-
- canEqual(Object) - Method in class CalculateHistogram
-
- canEqual(Object) - Method in class CalculateHistogramMasked
-
- canEqual(Object) - Method in class LabelledWithConfidence
-
- canEqual(Object) - Method in class WithConfidence
-
- canEqual(Object) - Method in class ChangeableOutputSequence
-
- canEqual(Object) - Method in class SortedSetChannel
-
- canEqual(Object) - Method in class SortedSetSlice
-
- canEqual(Object) - Method in class AllSlicesMaskEverythingNonZero
-
- canEqual(Object) - Method in class AllSlicesMaskNonZero
-
- canEqual(Object) - Method in class CenterSlice
-
- canEqual(Object) - Method in class CenterSliceBase
-
- canEqual(Object) - Method in class CenterSliceWindow
-
- canEqual(Object) - Method in class GreatestAreaSlice
-
- canEqual(Object) - Method in class IndexedRegionBase
-
- canEqual(Object) - Method in class SelectSlicesBase
-
- canEqual(Object) - Method in class SelectSlicesWithIndexBase
-
- canEqual(Object) - Method in class Specific
-
- canEqual(Object) - Method in class CalculateDeriveMarkCollectionInput
-
- canEqual(Object) - Method in class CalculateDeriveMarkInput
-
- canEqual(Object) - Method in class CalculateOverlap
-
- canEqual(Object) - Method in class CalculateOverlapMask
-
- canEqual(Object) - Method in class CalculateOverlapMIP
-
- canEqual(Object) - Method in class CalculateOverlapMIPBase
-
- canEqual(Object) - Method in class CalculateOverlapMIPRatio
-
- canEqual(Object) - Method in class HOGParameters
-
- canEqual(Object) - Method in class FitResult
-
- canEqual(Object) - Method in class CalculateEllipseLeastSquares
-
- canEqual(Object) - Method in class CalculateEllipsoidLeastSquares
-
- canEqual(Object) - Method in class Point3d
-
- canEqual(Object) - Method in class Point3f
-
- canEqual(Object) - Method in class Point3i
-
- canEqual(Object) - Method in class Tuple3d
-
- canEqual(Object) - Method in class Tuple3f
-
- canEqual(Object) - Method in class Tuple3i
-
- canEqual(Object) - Method in class Vector3d
-
- canExceptionBeCombined(Throwable) - Method in exception BeanMisconfiguredXmlException
-
- canExceptionBeCombined(Throwable) - Method in exception LocalisedBeanException
-
- canExceptionBeCombined(Throwable) - Method in exception AnchorCombinableException
-
- canExceptionBeCombined(Throwable) - Method in exception NamedProviderGetException
-
- canExceptionBeSkipped(Throwable) - Method in exception BeanMisconfiguredXmlException
-
- canExceptionBeSkipped(Throwable) - Method in exception LocalisedBeanException
-
- canExceptionBeSkipped(Throwable) - Method in exception AnchorCombinableException
-
- canExceptionBeSkipped(Throwable) - Method in exception NamedProviderGetException
-
- capacity() - Method in class UnsignedBuffer
-
- capacity() - Method in class VoxelBuffer
-
The capacity (i.e.
- capacity() - Method in class VoxelBufferUnsigned
-
- castTo() - Method in class VoxelsWrapper
-
Casts voxels to a particular type
- Cell - Class in org.anchoranalysis.image.bean.spatial.arrange
-
- Cell() - Constructor for class Cell
-
- CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
-
- CenterOfGravity(AxisType) - Constructor for class CenterOfGravity
-
Creates for a specific axis.
- CenterOfGravity() - Constructor for class CenterOfGravity
-
- centerOfGravity() - Method in class ObjectMask
-
Calculates center-of-gravity across all axes
- centerOfGravity(AxisType) - Method in class ObjectMask
-
Calculates center-of-gravity for one specific axis only
- centerOfGravity() - Method in class BoundingBox
-
- CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- CenterOnMask() - Constructor for class CenterOnMask
-
- centerPoint() - Method in class Mark
-
- centerPoint() - Method in class MarkWithPosition
-
- centerPoint() - Method in class LineSegment
-
- centerPoint() - Method in class PointList
-
- centerPoint() - Method in class Polygon
-
- centerPoint() - Method in class PolygonCurve
-
- centerPoint() - Method in class EllipseStandardFormConverter
-
- CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- CenterSlice() - Constructor for class CenterSlice
-
- CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- CenterSliceBase() - Constructor for class CenterSliceBase
-
- CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one
slice, specifically centerSlice+- windowSize
- CenterSliceWindow() - Constructor for class CenterSliceWindow
-
- chainCode(int, int, int) - Static method in class ChainCodesDirection
-
- chainCodes(int) - Method in class WatershedEncoding
-
Decodes a chain-code into a point
- ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
Maps directions to chain codes
- ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format
-
- ChangeableOutputSequence() - Constructor for class ChangeableOutputSequence
-
- changedMarkIDArray() - Method in class Kernel
-
The mark ids that were changed in the last energy calculation for the kernel
- changedMarkIDArray() - Method in class KernelBirth
-
- changedMarkIDArray() - Method in class KernelBirthAndKill
-
- changedMarkIDArray() - Method in class KernelDeath
-
- changedMarkIDArray() - Method in class KernelExchange
-
- changedMarkIDArray() - Method in class KernelInitialMarksFromPartition
-
- changedMarkIDArray() - Method in class KernelInitialMarksProposed
-
- changedMarkIDArray() - Method in class KernelInitialMarksVoxelized
-
- changedMarkIDArray() - Method in class KernelMerge
-
- changedMarkIDArray() - Method in class KernelReplace
-
- changedMarkIDArray() - Method in class KernelSplit
-
- changedOffset(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- changeExtension(Path, NonImageFileFormat, FileFormat) - Static method in class FormatExtensions
-
Change the extension in a path.
- changeExtent(Extent) - Method in class BoundingBox
-
- changeExtentZ(int) - Method in class BoundingBox
-
- changeInput(U) - Method in class InputBound
-
Immutably changes the input-object
- changeInputAndSharedState(U, V) - Method in class InputBound
-
Immutably changes the input-object and shared-state
- changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class IterateVoxelsAll
-
Changes each voxel, reading and writing the buffer as an int.
- changePrefix(DirectoryWithPrefix) - Method in class OutputterTarget
-
- changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class OutputterChecked
-
- changeZ(int, int) - Method in class BoundingBox
-
- Channel - Class in org.anchoranalysis.image.core.channel
-
A channel from an image.
- Channel(Voxels<?>, Optional<Resolution>) - Constructor for class Channel
-
Constructor
- channel() - Method in class Mask
-
The underlying channel which contains the binary-values.
- channel(String) - Static method in class ReferenceFactory
-
- channelAt(int) - Method in class RGBStack
-
- ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert
-
Converts a channel from one type to another specific type.
- ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class ChannelConverter
-
- ChannelConverterAttached<S,T> - Interface in org.anchoranalysis.image.core.channel.convert.attached
-
A channel-converter that has been permanently attached to a particular object.
- ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert
-
Converts a channel from one type to multiple other types.
- ChannelConverterMulti() - Constructor for class ChannelConverterMulti
-
- ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts a channel(s) at a particular timepoint into a stack(s).
- ChannelConvertStyle() - Constructor for class ChannelConvertStyle
-
- ChannelEntry - Class in org.anchoranalysis.image.io.bean.channel
-
- ChannelEntry(String, int) - Constructor for class ChannelEntry
-
- ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a channel for one of several data-types
- ChannelFactoryByte - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryByte() - Constructor for class ChannelFactoryByte
-
- ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryFloat() - Constructor for class ChannelFactoryFloat
-
- ChannelFactoryInt - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryInt() - Constructor for class ChannelFactoryInt
-
- ChannelFactoryShort - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryShort() - Constructor for class ChannelFactoryShort
-
- ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a channel for a specific data-type
- ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class ChannelFactorySingleType
-
- ChannelFilter - Class in org.anchoranalysis.image.io.bean.channel
-
Applies a filter to a particular channel
- ChannelFilter() - Constructor for class ChannelFilter
-
- ChannelGenerator - Class in org.anchoranalysis.image.io.channel.output
-
Writes a single channel to a file.
- ChannelGenerator(String) - Constructor for class ChannelGenerator
-
- ChannelGetter - Interface in org.anchoranalysis.image.io.channel.input
-
- ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.stack
-
- ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class ChannelGetterForTimepoint
-
- ChannelMap - Class in org.anchoranalysis.image.io.bean.channel
-
- ChannelMap() - Constructor for class ChannelMap
-
- ChannelMapper - Class in org.anchoranalysis.image.core.stack
-
Helps a retrieve channel and an associated converter and apply operation on them jointly
- ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class ChannelMapper
-
- channelNames() - Method in interface NamedChannelsForSeries
-
- channelNames() - Method in class NamedChannelsForSeriesConcatenate
-
- channelNames() - Method in class NamedChannelsForSeriesMap
-
- channelNames() - Method in interface OpenedImageFile
-
- channelNames() - Method in class BioformatsOpenedRaster
-
- channelNames() - Method in class MultiFileReaderOpenedRaster
-
- ChannelProvider - Class in org.anchoranalysis.image.bean.provider
-
- ChannelProvider() - Constructor for class ChannelProvider
-
- ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider
-
A channel-provider based-on two input channel-providers that must be of the same dimensionality
- ChannelProviderBinary() - Constructor for class ChannelProviderBinary
-
- ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider
-
- ChannelProviderTernary() - Constructor for class ChannelProviderTernary
-
- ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider
-
- ChannelProviderUnary() - Constructor for class ChannelProviderUnary
-
- channels() - Method in class ImageInitialization
-
- ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped
-
Source of channels for aggregating.
- ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>) - Constructor for class ChannelSource
-
- channelsPerByteArray(IFormatReader) - Method in class Default
-
- channelsPerByteArray(IFormatReader) - Method in class ForceChannelsPerByteArray
-
- channelsPerByteArray(IFormatReader) - Method in class ReadOptions
-
The number of channels returned with each call to IFormatReader.openBytes(int).
- channelsPerByteArray(IFormatReader) - Method in class ReadOptionsDelegate
-
- check(Mark, RegionMap, EnergyStack) - Method in class CheckMark
-
Checks a mark
- check(Channel, Mask) - Static method in class DimensionsChecker
-
- check(Channel, String, Dimensions) - Static method in class DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel
- check(Mask, String, Dimensions) - Static method in class DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel
- check(Mark, RegionMap, EnergyStack) - Method in class AndList
-
- check(Mark, RegionMap, EnergyStack) - Method in class AnySliceCenterOnMask
-
- check(Mark, RegionMap, EnergyStack) - Method in class CenterOnMask
-
- check(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
-
- check(Mark, RegionMap, EnergyStack) - Method in class Not
-
- check(Mark, RegionMap, EnergyStack) - Method in class RadiiMinRatio
-
- check(Mark, RegionMap, EnergyStack) - Method in class VolumeMin
-
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- Check() - Constructor for class Check
-
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- Check() - Constructor for class Check
-
- check(T) - Static method in class BeanTestChecker
-
Checks if a bean has all necessary items, throwing a run-time exception if it does not.
- checkAbsolutePath() - Method in class OutputPrefixerSettings
-
- checkAndInit(T, P, Logger) - Static method in class BeanTestChecker
-
- CheckCacheForSpecificChildren - Class in org.anchoranalysis.feature.session.cache.finder
-
For particular child-caches, check if a session-input is available from another LRU-cache and
reuse.
- CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class CheckCacheForSpecificChildren
-
- checkChannelType(VoxelDataType) - Method in class ConsistentChannelChecker
-
Checks that a channel has the same type (max value) as the others
- checkCompatibleWith(Mark) - Method in class KernelProposer
-
- CheckedBiConsumer<S,T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
BiConsumer but can also throw a checked exception.
- CheckedBiFunction<S,T,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
BiFunction but can also throw a checked exception.
- CheckedBooleanSupplier<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedConsumer<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Consumes a value and throws an exception
- CheckedFunction<S,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Function but can also thrown an exception.
- CheckedIntConsumer<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Consumes an int and throws an exception
- CheckedIntFunction<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedPredicate<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Predicate but can also throw an exception.
- CheckedProgressingSupplier<R,E extends Exception> - Interface in org.anchoranalysis.core.progress
-
Like
CheckedSupplier but can update a progress-reporter as the operation progresses.
- CheckedRunnable<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedStream - Class in org.anchoranalysis.core.functional
-
Map operations for streams that can throw checked-exceptions
- CheckedStream.ConvertedToRuntimeException - Exception in org.anchoranalysis.core.functional
-
An exception that wraps another exception, but exposes itself as a
RuntimeException
- CheckedSupplier<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Supplier but can also throw an exception.
- CheckedToDoubleBiFunction<T,U,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedToIntFunction<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedUnaryOperator<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckException - Exception in org.anchoranalysis.mpp.feature.error
-
- CheckException(String) - Constructor for exception CheckException
-
- CheckException(String, Throwable) - Constructor for exception CheckException
-
- CheckException(Throwable) - Constructor for exception CheckException
-
- checkExtentMatch(BoundingBox, BoundingBox) - Static method in class ExtentMatchHelper
-
- CheckIfAllowed - Class in org.anchoranalysis.io.output.writer
-
- CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class CheckIfAllowed
-
- checkIfConnected() - Method in class ObjectMask
-
Determines if an object-mask is connected.
- CheckMark - Class in org.anchoranalysis.mpp.feature.bean.mark
-
A predicate on a mark to check if a condition has been satisfied.
- CheckMark() - Constructor for class CheckMark
-
- CheckMarkWithMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- CheckMarkWithMask() - Constructor for class CheckMarkWithMask
-
- checkMisconfigured(BeanInstanceMap) - Method in class AnchorBean
-
Checks that a bean's properties conform to expectations.
- CheckMisconfigured - Class in org.anchoranalysis.bean.initializable
-
Routines for checking that particular patterns exist with bean-properties
- checkMisconfigured(BeanInstanceMap) - Method in class SequenceInteger
-
- checkMisconfigured(BeanInstanceMap) - Method in class FeatureEvaluator
-
- checkMisconfigured(BeanInstanceMap) - Method in class OutputWriteSettings
-
- checkMisconfigured(BeanInstanceMap) - Method in interface FeedbackReceiver
-
- checkMisconfigured(BeanInstanceMap) - Method in class FromStack
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExtractSliceRange
-
- checkMisconfigured(BeanInstanceMap) - Method in class Erode
-
- checkMisconfigured(BeanInstanceMap) - Method in class Sequence
-
- checkMisconfigured(BeanInstanceMap) - Method in class ThreeChannels
-
- checkMisconfigured(BeanInstanceMap) - Method in class ThreeColoredObjects
-
- checkMisconfigured(BeanInstanceMap) - Method in class FromChannelOrMask
-
- checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeature
-
- checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeatureSequenceInteger
-
- checkMisconfigured(BeanInstanceMap) - Method in class Intersection
-
- checkMisconfigured(BeanInstanceMap) - Method in class IntensityMeanShellBase
-
- checkMisconfigured(BeanInstanceMap) - Method in class LastDirectories
-
- checkMisconfigured(BeanInstanceMap) - Method in class CoupledManifestsInputManager
-
- checkMisconfigured(BeanInstanceMap) - Method in class HOGFeature
-
- checkMisconfigured(BeanInstanceMap) - Method in class FromDictionary
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickExperiment
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetExperiment
-
- checkMisconfigured(BeanInstanceMap) - Method in class MultiInputManagerQuick
-
- checkMisconfigured(BeanInstanceMap) - Method in class NamedChannelsQuick
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExperimentResultsExperimentStructure
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExperimentStructure
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetStructuredExperiment
-
- CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.file.group.check
-
- CheckParsedFilePathBag() - Constructor for class CheckParsedFilePathBag
-
- checkResultVector(ResultsVector) - Static method in class ConstantsInListFixture
-
checks that a result-vector has the results we expect from the feature-list associated with
this fixture
- checkSize(Extent) - Method in class HOGParameters
-
- checkUnsupported3D(Channel) - Static method in class SegmentChannelIntoObjects
-
- checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class SegmentChannelIntoObjects
-
- checkUnsupportedSeeds(Optional<SeedCollection>) - Static method in class SegmentChannelIntoObjects
-
- ChildCacheFinder - Interface in org.anchoranalysis.feature.session.cache.finder
-
Strategy to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
- childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface FeatureSessionCache
-
Gets/creates a child-cache for a given name
- childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class CheckCacheForSpecificChildren
-
- childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in interface ChildCacheFinder
-
Selects a child-cache given a parent and a child-name.
- childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class DefaultChildCacheFinder
-
- ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache
-
A unique identifier for a child-cache name, that uses a class and optionally additionally a
part-name
a class: guaranteed to be unique for the class
an optional part-name (string): a further division of the class into different caches
- ChildCacheName(Class<?>) - Constructor for class ChildCacheName
-
Uses only the class as an identifier - and a blank part-name
- ChildCacheName(Class<?>, int) - Constructor for class ChildCacheName
-
Uses only the class as an identifier - and a integer part-name
- ChildCacheName(Class<?>, String) - Constructor for class ChildCacheName
-
Uses both the class and a part-name as an identifier
- children() - Method in class ErrorNodeImpl
-
- ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- ChooseOneList() - Constructor for class ChooseOneList
-
- Circle - Class in org.anchoranalysis.mpp.mark.conic
-
A circle
- Circle(Bound) - Constructor for class Circle
-
Creates with a radius within particular bounds.
- Circle(Circle) - Constructor for class Circle
-
Copy constructor
- Circle() - Constructor for class Circle
-
- circleAt(Point2i, double) - Static method in class CircleObjectFixture
-
- CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
-
- circumference(int) - Method in class Ellipse
-
- clamp(Point3i, Dimensions) - Static method in class PointClamper
-
- clamp(Point3d, Dimensions) - Static method in class PointClamper
-
- ClampHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
- ClampHistogramMax() - Constructor for class ClampHistogramMax
-
- clampTo(Extent) - Method in class BoundingBox
-
- classificationString(boolean) - Static method in class BinaryOutcomeImageLabeller
-
- classInCurrentJar() - Method in class LauncherConfig
-
a class which we use to determine the base location for pathRelativeProperties
- clean() - Method in class VoxelizedMarksWithEnergy
-
- clean() - Method in class EnergyMemoList
-
- cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByChannel
-
- cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByRegion
-
- cleanUp(VoxelPartitionFactory<T>) - Method in interface VoxelPartition
-
- cleanUp(VoxelPartitionFactory<Histogram>) - Method in class VoxelPartitionHistogram
-
- cleanUp() - Method in interface VoxelizedMark
-
- clear() - Method in class FeatureList
-
- clear() - Method in class StackNotUniformSized
-
- clear() - Method in class UnsignedBuffer
-
- clear() - Method in class ObjectCollection
-
- clear() - Method in class UpdatableMarksList
-
- clearBest() - Method in class DualState
-
- clipTo(T, Extent) - Method in interface AccessObjectMask
-
Ensures the element lies within a certain extent.
- clipTo(Extent) - Method in class ObjectMask
-
Makes sure an object fits inside an extent, removing any parts which do not.
- close() - Method in interface Progress
-
- close() - Method in class ProgressConsole
-
- close() - Method in class ProgressIgnore
-
- close() - Method in class ProgressIncrement
-
- close() - Method in class ProgressMultiple
-
- close() - Method in class ProgressOneOfMany
-
- close(boolean, boolean) - Method in class StatefulNullMessageLogger
-
- close(boolean, boolean) - Method in class ConsoleMessageLogger
-
- close(boolean, boolean) - Method in class FailureOnlyMessageLogger
-
- close(boolean, boolean) - Method in class MessageLoggerList
-
- close(boolean, boolean) - Method in interface StatefulMessageLogger
-
- close(boolean, boolean) - Method in class TextFileMessageLogger
-
- close() - Method in class FeatureCSVWriter
-
Closes any open file-handles.
- close() - Method in class ResultsWriter
-
- close() - Method in interface OpenedImageFile
-
- close() - Method in class BioformatsOpenedRaster
-
- close() - Method in class CSVWriter
-
- close() - Method in class CSVReader.OpenedCSVFile
-
- close() - Method in class ReadByLine
-
Closes any opened-files
- close(ErrorReporter) - Method in interface InputFromManager
-
Performs all tidying up, file-closing etc.
- close(ErrorReporter) - Method in class InputFromManagerDelegate
-
- close(ErrorReporter) - Method in class MultiInput
-
- close(ErrorReporter) - Method in class StackWithMap
-
- close() - Method in class SharedStateFilteredImageOutput
-
- close() - Method in class SharedStateSelectedSlice
-
- close() - Method in class MultiFileReaderOpenedRaster
-
- closeAnyOpenIO() - Method in class SharedStateExportFeatures
-
- closeAnyOpenIO() - Method in class SharedStateSegmentInstance
-
- closeLogger() - Method in class RecordingCounter
-
Closes the logger.
- closestPointOnBorder(Point3d) - Method in class BoundingBox
-
- CODE_MINIMA - Static variable in class WatershedEncoding
-
- CODE_PLATEAU - Static variable in class WatershedEncoding
-
- CODE_TEMPORARY - Static variable in class WatershedEncoding
-
- CODE_UNVISITED - Static variable in class WatershedEncoding
-
- CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CoefficientOfVarianceFromAll() - Constructor for class CoefficientOfVarianceFromAll
-
- coefficientOfVariation(Histogram) - Static method in class HistogramStatistics
-
- CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- CoefficientOfVariation() - Constructor for class CoefficientOfVariation
-
- CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
-
Removes the file-name from a path, but keeps the directories and preserves the file-extension.
- CollapseFileName() - Constructor for class CollapseFileName
-
- CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection
-
Writes a collection of elements as a subdirectory with each element as a single file in the
subdirectory.
- CollectionGenerator(Generator<T>, String) - Constructor for class CollectionGenerator
-
- collectResult() - Method in interface ProcessChangedPointAbsoluteMasked
-
Collects the result of the operation after processing neighbor pixels
- collectResult() - Method in interface ProcessVoxelNeighbor
-
Collects the result of the operation after processing neighbor pixels
- collectResult() - Method in interface ProcessVoxelNeighborAbsolute
-
Collects the result of the operation after processing neighbor pixels
- collectResult() - Method in class WrapAbsoluteAsMasked
-
- colorAxis(Axis) - Method in class PlotColorScheme
-
- colorChart(JFreeChart) - Method in class PlotColorScheme
-
- ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.color
-
Converts a RGB stack into another color space using OpenCV
- ColorConverterBase() - Constructor for class ColorConverterBase
-
- ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Base class for providers that draw entities (an outline or filled) on a background
- ColoredBase() - Constructor for class ColoredBase
-
- ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Like
ColoredBase but uses a generator to determine the colors for the objects
- ColoredBaseWithGenerator() - Constructor for class ColoredBaseWithGenerator
-
- ColoredMarks - Class in org.anchoranalysis.mpp.mark
-
- ColoredMarks() - Constructor for class ColoredMarks
-
- ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter<Mark>) - Constructor for class ColoredMarks
-
- ColoredMarks(Mark, RGBColor) - Constructor for class ColoredMarks
-
- ColoredMarks(MarkCollection, ColorList) - Constructor for class ColoredMarks
-
- ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider
-
Draws a colored representation (outline or filled) of an
MarkCollection on a background
- ColoredMarks() - Constructor for class ColoredMarks
-
- ColoredMarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
-
- ColoredMarksWithDisplayStack(MarksWithDisplayStack, ColorIndex, IdentifierGetter<Mark>) - Constructor for class ColoredMarksWithDisplayStack
-
- ColoredMarksWithDisplayStack(ColoredMarks, DisplayStack) - Constructor for class ColoredMarksWithDisplayStack
-
- ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Draws a colored representation (outline or filled) of a
ObjectMask on a background
- ColoredMask() - Constructor for class ColoredMask
-
- ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object
-
- ColoredObjectCollection() - Constructor for class ColoredObjectCollection
-
Create with an empty collection.
- ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class ColoredObjectCollection
-
Create with a single object and color.
- ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class ColoredObjectCollection
-
Create with an existing object and color list.
- ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Draws a colored representation (outline or filled) of an
ObjectCollection on a background
- ColoredObjects() - Constructor for class ColoredObjects
-
- coloredObjectsToDraw(Dimensions) - Method in class ColoredBase
-
Creates colored-objects to be drawn
- coloredObjectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator
-
- coloredObjectsToDraw(Dimensions) - Method in class ColoredMask
-
- coloredObjectsToDraw(Dimensions) - Method in class ThreeColoredObjects
-
- ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection
-
- ColoredOverlayCollection() - Constructor for class ColoredOverlayCollection
-
- ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class ColoredOverlayCollection
-
- colorFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes
-
A color for a particular object
- colorForEachIndex(int) - Method in class ColorScheme
-
Assigns a color to each index value from a list of size numberColors.
- ColorIndex - Interface in org.anchoranalysis.core.color
-
- ColorIndexModulo - Class in org.anchoranalysis.core.color
-
- ColorIndexModulo(ColorIndex) - Constructor for class ColorIndexModulo
-
- colorLegend(LegendTitle) - Method in class PlotColorScheme
-
- ColorList - Class in org.anchoranalysis.core.color
-
- ColorList(Color...) - Constructor for class ColorList
-
- ColorList(RGBColor...) - Constructor for class ColorList
-
- ColorList(RGBColor) - Constructor for class ColorList
-
- ColorList() - Constructor for class ColorList
-
- colorPlot(XYPlot) - Method in class PlotColorScheme
-
- colorPlot(CategoryPlot) - Method in class PlotColorScheme
-
- ColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator
-
- ColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class ColorPool
-
- ColorProvider - Class in org.anchoranalysis.image.bean.provider
-
Provides a list of one or more colors
- ColorProvider() - Constructor for class ColorProvider
-
- ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme
-
Creates a set of related colors.
- ColorScheme() - Constructor for class ColorScheme
-
- ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme
-
- ColorSchemeUnary() - Constructor for class ColorSchemeUnary
-
- ColorSchemeUnary(ColorScheme) - Constructor for class ColorSchemeUnary
-
- colorSpaceCode() - Method in class ColorConverterBase
-
The color space conversion code to use from OpenCV
- colorSpaceCode() - Method in class ConvertRGBToHSV
-
- colorSpaceCode() - Method in class ConvertRGBToLab
-
- column(int) - Method in class RotationMatrix
-
- ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- ColumnDefinition() - Constructor for class ColumnDefinition
-
- combine(Path, Path) - Static method in class BeanPathUtilities
-
- Combine - Class in org.anchoranalysis.image.io.bean.object.draw
-
- Combine() - Constructor for class Combine
-
- Combine(List<DrawObject>) - Constructor for class Combine
-
- combine(boolean, boolean) - Method in class MultiLevelAnd
-
- combine(boolean, boolean) - Method in class MultiLevelBinary
-
- combine(boolean, boolean) - Method in class MultiLevelOr
-
- combine(boolean, boolean) - Method in class SingleLevelAnd
-
- combine(boolean, boolean) - Method in class SingleLevelBinary
-
- combine(boolean, boolean) - Method in class SingleLevelOr
-
- Combine - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- Combine() - Constructor for class Combine
-
- CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
- CombineBase() - Constructor for class CombineBase
-
- CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task
-
Combines multiple CSV files into a single CSV file.
- CombineCSV() - Constructor for class CombineCSV
-
- combined() - Method in class PathDifference
-
The directory-component (if it exists) and filename-component combined.
- combined() - Method in class SplitPath
-
- CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined
-
Several generators combined together with a common element-type.
- CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator(Generator<T>...) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator() - Constructor for class CombinedListGenerator
-
- CombinedName - Class in org.anchoranalysis.feature.io.name
-
A name which is unique when a primaryName is combined with a secondaryName
- CombinedName(String, String) - Constructor for class CombinedName
-
Creates with explicit strings for both parts.
- combineDscr(String, String) - Method in class AddConstantTo
-
- combineDscr(String, String) - Method in class ConstantToThePowerOf
-
- combineDscr(String, String) - Method in class DivideByConstant
-
- combineDscr(String, String) - Method in class MultiplyByConstant
-
- combineDscr(String, String) - Method in class SubtractFrom
-
- combineDscr(String, String) - Method in class ToThePowerOfConstant
-
- combineDscr(String, String) - Method in class ReplaceUnusualValue
-
- combineDscr(String, String) - Method in class WithValueBase
-
- combineDscrsRecursively(String, String) - Method in exception AnchorCombinableException
-
Traverses through a set of nested-exceptions creating a description for each "combined"
exception, and combining them into a single string.
- CombineObjectsForFeatures<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
-
A way to combine (or not combine) objects so that they provide a feature-table.
- CombineObjectsForFeatures() - Constructor for class CombineObjectsForFeatures
-
- CombineRasterGenerator<T> - Class in org.anchoranalysis.image.io.bean.stack.combine
-
Combines a number of generators of Raster images by tiling their outputs together
- CombineRasterGenerator() - Constructor for class CombineRasterGenerator
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelAnd
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelBinary
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelOr
-
- CombineToOnePath - Class in org.anchoranalysis.image.core.outline.traverser.path.merge
-
- combineToOnePath(List<ContiguousVoxelPath>) - Static method in class CombineToOnePath
-
Combines all the contiguous paths to a single-path
- combineToOnePath() - Method in class VisitedVoxels
-
Combines all the contiguous paths to a single-path
- CombineTypes - Class in org.anchoranalysis.image.voxel.datatype
-
- combineTypes(VoxelDataType, VoxelDataType) - Static method in class CombineTypes
-
- combineValueAndFeature(double, double) - Method in class AddConstantTo
-
- combineValueAndFeature(double, double) - Method in class ConstantToThePowerOf
-
- combineValueAndFeature(double, double) - Method in class DivideByConstant
-
- combineValueAndFeature(double, double) - Method in class MultiplyByConstant
-
- combineValueAndFeature(double, double) - Method in class SubtractFrom
-
- combineValueAndFeature(double, double) - Method in class ToThePowerOfConstant
-
- combineValueAndFeature(double, double) - Method in class ReplaceUnusualValue
-
- combineValueAndFeature(double, double) - Method in class WithValueBase
-
- combineWithSuffix(String) - Method in class FilenameSplitExtension
-
Inserts a suffix after the base-name, but before the extension, immutably.
- CommandLineException - Exception in org.anchoranalysis.launcher
-
An exception thrown at run-time while processing command-line args
- CommandLineException(String) - Constructor for exception CommandLineException
-
- CommandLineExtracter - Class in org.anchoranalysis.launcher.options
-
Adds methods to CommandLine for querying and extracting options, with and without
arguments.
- CommandLineExtracter(CommandLine) - Constructor for class CommandLineExtracter
-
- CommandLineOptions - Class in org.anchoranalysis.launcher.options
-
All command-line options used by the launcher.
- common() - Method in class InitializationContext
-
- common() - Method in interface InputOutputContext
-
Creates a
CommonContext a context that contains a subset of this context.
- CommonContext - Class in org.anchoranalysis.core.log
-
A logger with additional configuration that are coupled together widely in the code
- CommonContext(Logger, Path) - Constructor for class CommonContext
-
- CommonPath - Class in org.anchoranalysis.core.system.path
-
Finds the common root directory of a set of paths.
- commonType(Stream<VoxelDataType>) - Static method in class FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} of a stream of types.
- commonType(VoxelDataType, VoxelDataType) - Static method in class FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} both first and
second.
- Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point
-
- Comparator3d() - Constructor for class Comparator3d
-
- Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point
-
- Comparator3i() - Constructor for class Comparator3i
-
- ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name
-
Orders two name-values by their name (alphabetic order from standard String.compareTo(String))
- ComparatorOrderByName() - Constructor for class ComparatorOrderByName
-
- compare(NameValue<V>, NameValue<V>) - Method in class ComparatorOrderByName
-
- compare(T, T) - Method in class Comparator3d
-
- compare(T, T) - Method in class Comparator3i
-
- CompareAnnotations<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
Task to compare a set of annotations to a segmentation or another set of annotations.
- CompareAnnotations() - Constructor for class CompareAnnotations
-
- Comparer - Class in org.anchoranalysis.annotation.io.bean.comparer
-
- Comparer() - Constructor for class Comparer
-
- compareTo(WithPriority<T>) - Method in class WithPriority
-
Orders so that hasPriority==true has higher priority in queue to hasPriority==false
- compareTo(IndexGetter) - Method in class Indexable
-
- compareTo(MultiName) - Method in class CombinedName
-
- compareTo(MultiName) - Method in class SimpleName
-
- compareTo(EigenvalueAndVector) - Method in class EigenvalueAndVector
-
- compareTo(LabelledWithConfidence<T>) - Method in class LabelledWithConfidence
-
- compareTo(WithConfidence<T>) - Method in class WithConfidence
-
- compareTo(SortedSetChannel) - Method in class SortedSetChannel
-
- compareTo(SortedSetSlice) - Method in class SortedSetSlice
-
- compareTo(BoundingBox) - Method in class BoundingBox
-
- compareTo(Extent) - Method in class Extent
-
- compareTo(ReadableTuple3i) - Method in interface ReadableTuple3i
-
- CompareWithRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Compares a value with a range, returning specified constants if its inside the range, below it or
above it
- CompareWithRange() - Constructor for class CompareWithRange
-
- CompareWithRangeFeature<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
- CompareWithRangeFeature() - Constructor for class CompareWithRangeFeature
-
- CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
-
- completeProjection() - Method in interface ProjectableBuffer
-
Performs any final operation before turning the projected buffer.
- Compose<S,T,U> - Class in org.anchoranalysis.mpp.segment.transformer
-
Combines a transformation from S to U with one from U to T
- Compose() - Constructor for class Compose
-
- Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class Compose
-
- CompressAnyTIFF - Class in org.anchoranalysis.plugin.io.bean.file.copy.method
-
Create a voxelwise
compressed copy of any TIFF file being copied, and otherwise do a
Bytewise copy.
- CompressAnyTIFF() - Constructor for class CompressAnyTIFF
-
- computeInitialFeasibleSolution() - Method in class HungarianAlgorithm
-
Compute an initial feasible solution by assigning zero labels to the workers and by assigning
to each job a label equal to the minimum cost among its incident edges.
- Concatenate - Class in org.anchoranalysis.bean.define.adder
-
Concatenates a list of adders
- Concatenate() - Constructor for class Concatenate
-
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider
-
- Concatenate() - Constructor for class Concatenate
-
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
- Concatenate() - Constructor for class Concatenate
-
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider
-
Combines all the channels from one or more sources (stacks, channels etc.)
- Concatenate() - Constructor for class Concatenate
-
- Concatenate<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Concatenates several input-managers
- Concatenate() - Constructor for class Concatenate
-
- ConcatenateFileTypes - Class in org.anchoranalysis.io.generator
-
Concatenates the arrays of
FileType that may be returned from write operations.
- ConcatenateFileTypes() - Constructor for class ConcatenateFileTypes
-
Creates to always use a list for tracking.
- ConcatenateFileTypes(boolean) - Constructor for class ConcatenateFileTypes
-
- ConcurrencyPlan - Class in org.anchoranalysis.core.concurrency
-
How many allocated CPUS and CPUs can be used.
- ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
-
- ConcurrentJobMonitor(long) - Constructor for class ConcurrentJobMonitor
-
- ConcurrentModelException - Exception in org.anchoranalysis.core.concurrency
-
This exception indicates that an error occurred when performing inference from a model
concurrently.
- ConcurrentModelException(Throwable) - Constructor for exception ConcurrentModelException
-
- ConcurrentModelPool<T> - Class in org.anchoranalysis.core.concurrency
-
Keeps concurrent copies of a model to be used by different threads.
- ConcurrentModelPool(ConcurrencyPlan, ConcurrentModelPool.CreateModelForPool<T>) - Constructor for class ConcurrentModelPool
-
- ConcurrentModelPool.CreateModelForPool<T> - Interface in org.anchoranalysis.core.concurrency
-
Creates a model to use in the pool
- ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel
-
Executes another
BinaryKernel iff a predicated is satisfied for a particular point.
- ConditionalKernel(BinaryKernel, Predicate<Point3i>) - Constructor for class ConditionalKernel
-
- ConditionallyMergeOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Where objects overlap, they are merged together if certain conditions are fulfilled.
- ConditionallyMergeOverlappingObjects() - Constructor for class ConditionallyMergeOverlappingObjects
-
- ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats
-
Singleton class for making sure Bioformats is configured configured.
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteDivideByParam
-
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger
-
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFirstSecondOrder
-
- ConicBase - Class in org.anchoranalysis.mpp.mark.conic
-
- ConicBase() - Constructor for class ConicBase
-
- ConicBase(MarkWithPosition) - Constructor for class ConicBase
-
- ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter
-
- ConicFitterBase() - Constructor for class ConicFitterBase
-
- ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Performs a binary-segmentation of the channel and converts its connected-components into objects
- ConnectedComponentsFromBinarySegmentation() - Constructor for class ConnectedComponentsFromBinarySegmentation
-
- ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Converts a binary-mask into its connected components
- ConnectedComponentsFromMask() - Constructor for class ConnectedComponentsFromMask
-
- connectedTo(Contour) - Method in class Contour
-
- connectedToFirstPointOf(Contour) - Method in class Contour
-
- connectedToLastPointOf(Contour) - Method in class Contour
-
- ConsiderVisit - Interface in org.anchoranalysis.image.core.outline.traverser
-
- considerVisit(Point3i, int) - Method in interface ConsiderVisit
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitScheduler
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerAnd
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerConvexAboutRoot
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerUniformSample
-
- ConsistentChannelChecker - Class in org.anchoranalysis.plugin.image.task.grouped
-
Checks that the histograms created from channels all have the same data type, res, max-value etc.
- ConsistentChannelChecker() - Constructor for class ConsistentChannelChecker
-
- ConsoleAccepted - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- ConsoleAccepted() - Constructor for class ConsoleAccepted
-
- ConsoleAggregatedReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- ConsoleAggregatedReporter(double) - Constructor for class ConsoleAggregatedReporter
-
- ConsoleAggregatedReporter() - Constructor for class ConsoleAggregatedReporter
-
- ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log
-
- ConsoleMessageLogger() - Constructor for class ConsoleMessageLogger
-
- Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
- Constant(double) - Constructor for class Constant
-
Constructor with a particular value
- Constant(String, double) - Constructor for class Constant
-
Constructor with a particular value and a custom-name
- Constant() - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
A constant value for thresholding
- Constant() - Constructor for class Constant
-
- Constant(int) - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Always generates a constant path irrespective of the the input
- Constant() - Constructor for class Constant
-
- Constant(String) - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- Constant() - Constructor for class Constant
-
- ConstantScaleFactor - Class in org.anchoranalysis.plugin.image.bean.scale
-
- ConstantScaleFactor() - Constructor for class ConstantScaleFactor
-
- ConstantsInListFixture - Class in org.anchoranalysis.test.feature
-
- ConstantToThePowerOf<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- ConstantToThePowerOf() - Constructor for class ConstantToThePowerOf
-
- ConstantWeight - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
-
All marks have weight of 1
- ConstantWeight() - Constructor for class ConstantWeight
-
- containerOptional() - Method in class WithContainerBase
-
- containerRequired() - Method in class WithContainerBase
-
- contains(String) - Method in interface StringBeanCollection
-
- contains(String) - Method in class StringList
-
- contains(String) - Method in class StringSet
-
- contains(ChildCacheName) - Method in class CacheTransferSourceCollection
-
- contains(Feature<FeatureInput>) - Method in class SharedFeatureMulti
-
- contains(Point3d) - Method in class Dimensions
-
- contains(Point3i) - Method in class Dimensions
-
- contains(BoundingBox) - Method in class Dimensions
-
- contains(Point3i) - Method in class IntersectingObjects
-
All elements that contain a particular point.
- contains(Point3i) - Method in class ObjectMask
-
- contains(double) - Method in class ResolvedBound
-
- contains(Object) - Method in class UpdatableMarksList
-
- contains(Object) - Method in class MarkCollection
-
- contains() - Method in class BoundingBox
-
For evaluating whether this bounding-box contains other points, boxes etc.?
- contains(Point2i) - Method in class Extent
-
- contains(Point3d) - Method in class Extent
-
- contains(ReadableTuple3i) - Method in class Extent
-
- contains(int, int, int) - Method in class Extent
-
- contains(BoundingBox) - Method in class Extent
-
- contains(ReadableTuple3i) - Method in class RTree
-
Which bounding-boxes contain a particular point?
- containsAll(Collection<?>) - Method in class UpdatableMarksList
-
- containsChild(ChildCacheName) - Method in class CacheTransferSource
-
- containsEdge(V, V) - Method in class GraphWithoutPayload
-
Does the graph contain a particular edge?
- containsEdge(V, V) - Method in class GraphWithPayload
-
Does the graph contain a particular edge?
- containsKey(Class<?>) - Method in class BeanInstanceMap
-
- containsKey(String) - Method in class Dictionary
-
Does a parameter exist with a particular key?
- containsMark(Mark) - Method in class RandomCollectionWithAddCriteria
-
- containsOrEmpty() - Method in class DebugModeParams
-
- containsStream(ReadableTuple3i) - Method in class RTree
-
- containsVertex(V) - Method in class GraphWithoutPayload
-
Does the graph contain a particular vertex?
- containsVertex(V) - Method in class GraphWithPayload
-
Does the graph contain a particular vertex?
- containsX(double) - Method in class Extent
-
- containsX(int) - Method in class Extent
-
- containsY(double) - Method in class Extent
-
- containsY(int) - Method in class Extent
-
- containsZ(double) - Method in class Extent
-
- containsZ(int) - Method in class Extent
-
- ContiguousVoxelPath - Class in org.anchoranalysis.image.core.outline.traverser.path
-
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
- ContiguousVoxelPath(Point3i, Point3i) - Constructor for class ContiguousVoxelPath
-
With a single initial-point, and maybe a connection point
- ContiguousVoxelPath() - Constructor for class ContiguousVoxelPath
-
Without any connection-point
- continueFurther(int, double, int, MessageLogger) - Method in class TerminationCondition
-
Whether to continue for an additional iteration step or not.
- continueFurther(int, double, int, MessageLogger) - Method in class TerminationConditionListOr
-
- continueFurther(int, double, int, MessageLogger) - Method in class TriggerTerminationCondition
-
- continueFurther(int, double, int, MessageLogger) - Method in class NumberIterations
-
- continueFurther(int, double, int, MessageLogger) - Method in class UnchangedBase
-
- Contour - Class in org.anchoranalysis.spatial
-
A path of successively-neighbored points.
- Contour() - Constructor for class Contour
-
- contoursForObject(ObjectMask) - Static method in class CVFindContours
-
- ConversionPolicy - Enum in org.anchoranalysis.image.core.channel.convert
-
- convert(Channel, ConversionPolicy) - Method in class MaxIntensity
-
- convert(Channel, ConversionPolicy) - Method in interface ChannelConverterAttached
-
- convert(Channel, ConversionPolicy) - Method in class MaxIntensityFromHistogram
-
- convert(Channel, ConversionPolicy) - Method in class QuantileIntensityFromHistogram
-
- convert(Channel, ConversionPolicy) - Method in class UpperLowerQuantileIntensityFromHistogram
-
- convert(Stack, ConversionPolicy) - Method in class ChannelConverter
-
- convert(Channel, ConversionPolicy) - Method in class ChannelConverter
-
Converts channelIn to have voxels with data-type T.
- convert(Channel, VoxelDataType) - Method in class ChannelConverterMulti
-
- convert(DisplayStack) - Static method in class ConvertDisplayStackToRGB
-
- convert(ByteBuffer, int) - Method in class ToUnsignedByte
-
- convert(ByteBuffer, int) - Method in class UnsignedByteFromFloat
-
- convert(ByteBuffer, int) - Method in class UnsignedByteFromUnsignedByteInterleaving
-
- convert(ByteBuffer, int) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
-
- convert(ByteBuffer, int) - Method in class UnsignedByteFromUnsignedInt
-
- convert(ByteBuffer, int) - Method in class UnsignedByteFromUnsignedShort
-
- Convert<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel by applying a converter (no histogram is involved in the conversion).
- Convert() - Constructor for class Convert
-
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class ChannelConvertStyle
-
Converts a particular set of channels.
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class IndependentChannels
-
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class RGB
-
- convert(int) - Method in class NumberToStringConverter
-
Converts number to a string, padding with leading zeros if necessary to ensure the
desired width.
- convert2iTo3d(List<Point2i>) - Static method in class PointConverter
-
- convert2iTo3f(List<Point2i>) - Static method in class PointConverter
-
- convert3dTo3f(List<Point3d>) - Static method in class PointConverter
-
- convert3fTo3d(List<Point3f>) - Static method in class PointConverter
-
- convert3i(List<Point3f>, boolean) - Static method in class PointConverter
-
- convert3i(List<Point3d>) - Static method in class PointConverter
-
- convert3iTo3f(List<Point3i>) - Static method in class PointConverter
-
- ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
- ConvertBase() - Constructor for class ConvertBase
-
- convertBeforeAssign(DisplayStack) - Method in class DisplayStackGenerator
-
- convertBeforeAssign(Stack) - Method in class FlattenStackGenerator
-
- convertBeforeAssign(T) - Method in class RasterGeneratorBridge
-
- convertBeforeAssign(T) - Method in class RasterGeneratorDelegateToRaster
-
Converts an element before setting it on the delegate.
- convertBeforeTransform(Stack) - Method in class DisplayStackGenerator
-
- convertBeforeTransform(Stack) - Method in class FlattenStackGenerator
-
- convertBeforeTransform(Stack) - Method in class RasterGeneratorBridge
-
- convertBeforeTransform(Stack) - Method in class RasterGeneratorDelegateToRaster
-
- ConvertChannelTo<T> - Class in org.anchoranalysis.image.bean.channel.converter
-
Converts a channel from one type to another.
- ConvertChannelTo() - Constructor for class ConvertChannelTo
-
- ConvertChannelToWithHistogram<T> - Class in org.anchoranalysis.image.bean.channel.converter
-
Creates a
ChannelConverterAttached<Histogram, T> for converting a channel to a particular
type, making use of a
Histogram.
- ConvertChannelToWithHistogram() - Constructor for class ConvertChannelToWithHistogram
-
- convertCode(int, int, EncodedVoxels, Point3i) - Method in class EncodedIntBuffer
-
Convert code to connected-component
- convertCropped(DisplayStack, BoundingBox) - Static method in class ConvertDisplayStackToRGB
-
- ConvertDisplayStackToRGB - Class in org.anchoranalysis.image.io.stack
-
- ConvertedToRuntimeException(Throwable) - Constructor for exception CheckedStream.ConvertedToRuntimeException
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
-
- convertFloat(FloatBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertFloat(FloatBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
FloatBuffer to the current position in
a buffer of type
T.
- convertFrom(VoxelsWrapper, VoxelsFactoryTypeBound<T>) - Method in class VoxelsConverter
-
Creates a new voxels of type T and copies the voxels from from.
- ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts an ImagePlus into a channel or voxels.
- ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert
-
- ConvertFromPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertFromPhysicalVolume() - Constructor for class ConvertFromPhysicalVolume
-
- convertFromUnits(double, String) - Static method in class SpatialUnits
-
Converts a value from another unit-type to base units.
- convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
Converts a value from another unit-type to base units.
- ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format
-
Converts each input-image to an output format, optionally changing the bit depth.
- ConvertImageFormat() - Constructor for class ConvertImageFormat
-
- convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class FloatFromUnsignedByte
-
- convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class FloatFromUnsignedInt
-
- convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class ToFloat
-
- ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager> - Class in org.anchoranalysis.plugin.mpp.experiment.bean
-
- ConvertNamedChannels() - Constructor for class ConvertNamedChannels
-
- ConvertNamedChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- ConvertNamedChannelsInputToStack(NamedChannelsInput) - Constructor for class ConvertNamedChannelsInputToStack
-
Create with an input.
- ConvertNamedChannelsInputToStack(NamedChannelsInput, int, Optional<String>) - Constructor for class ConvertNamedChannelsInputToStack
-
Create with an input.
- ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- ConvertNamedChannelsToStack() - Constructor for class ConvertNamedChannelsToStack
-
- ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.color
-
- ConvertRGBToHSV() - Constructor for class ConvertRGBToHSV
-
- ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.color
-
- ConvertRGBToLab() - Constructor for class ConvertRGBToLab
-
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class ConvertTo
-
Converts a slice of single-channel into a newly created
VoxelBuffer.
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class ToUnsignedByte
-
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class ToFloat
-
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class UnsignedIntFromUnsignedInt
-
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class ToUnsignedShort
-
- ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Converts a subset of raw voxel bytes in a ByteBuffer to one or more destination channels.
- ConvertTo(Function<VoxelsWrapper, Voxels<T>>) - Constructor for class ConvertTo
-
- convertTo3d(Point2d) - Static method in class PointConverter
-
- convertTo3i(Point2i) - Static method in class PointConverter
-
- convertTo3i(Point2i, int) - Static method in class PointConverter
-
- ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert
-
- ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts a channel or voxels into a ImagePlus.
- ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert
-
Converts other voxel data-structures (as used by Anchor) to an ImageJ ImageProcessor.
- ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
-
- ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert
-
Converts common image data-structures used by Anchor to the Mat class used by OpenCV.
- ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
-
- convertToObjects(Dimensions) - Method in interface AnnotationWithMarks
-
Creates an object-collection that is a voxelized representation of the marks in the
annotation.
- convertToOutputType(Channel) - Method in class GradientBase
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertFromPhysicalVolume
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalAreaXY
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalDistance
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalVolume
-
- convertToPhysical(double, UnitConverter) - Method in class FeatureConvertUnits
-
- ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
- ConvertToPhysicalAreaXY() - Constructor for class ConvertToPhysicalAreaXY
-
- ConvertToPhysicalDistance<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
- ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class ConvertToPhysicalDistance
-
- ConvertToPhysicalDistance() - Constructor for class ConvertToPhysicalDistance
-
- ConvertToPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertToPhysicalVolume() - Constructor for class ConvertToPhysicalVolume
-
- convertToUnits(double, String) - Static method in class SpatialUnits
-
Converts a value in base-units to another unit-type.
- convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
Converts a value in base-units to another unit-type.
- ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert
-
Converts a ImageProcessor to a voxel-buffer of particular data-type.
- ConvertUnits<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.physical
-
- ConvertUnits() - Constructor for class ConvertUnits
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class ToByte
-
- convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertUnsignedByte(UnsignedByteBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedByteBuffer to the current
position in a buffer of type
T.
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
-
- convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertUnsignedInt(UnsignedIntBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedIntBuffer to the current
position in a buffer of type
T.
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
-
- convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertUnsignedShort(UnsignedShortBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedShortBuffer to the current
position in a buffer of type
T.
- convertValue(short) - Method in class ToUnsignedShort
-
- convertValue(short) - Method in class UnsignedShortFromSignedShort
-
- convertValue(short) - Method in class UnsignedShortFromUnsignedShort
-
- ConvertWithHistogram<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
- ConvertWithHistogram() - Constructor for class ConvertWithHistogram
-
- ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
- ConvexHull2D() - Constructor for class ConvexHull2D
-
- convexHull2D(List<Point2i>) - Static method in class ConvexHullUtilities
-
- convexHull2D(List<Point2i>, int) - Static method in class ConvexHullUtilities
-
Apply a convex-hull algorithm to filter a set of points.
- ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
- ConvexHull3D() - Constructor for class ConvexHull3D
-
- ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
- ConvexHullBase() - Constructor for class ConvexHullBase
-
- ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull
-
- copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, int) - Method in class ConvertTo
-
- copyAllFrames(IFormatReader, List<Channel>, Progress, ImageFileShape, ConvertTo<?>, ReadOptions) - Static method in class CopyConvert
-
Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels
converting them if necessary along the way
- copyBufferIndexTo(T, int, T, int) - Method in class Base
-
- copyChange(MarkCollection) - Method in class MarksFromPartition
-
Makes a copy, with different marks
- copyChangeIterationsDilation(int) - Method in class MorphologicalIterations
-
Copies the bean setting an new value for iterationsDilation
- copyChangeParams(Dictionary) - Method in class EnergyStack
-
- CopyContext<T> - Class in org.anchoranalysis.plugin.io.input.path
-
Context parameters when copying many files from a source directory to a destination directory.
- CopyContext(Path, Path, T) - Constructor for class CopyContext
-
- CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Copies the bytes from a IFormatReader to a list of channels, converting if necessary.
- CopyFiles<T> - Class in org.anchoranalysis.plugin.io.bean.task
-
Copy files to the output-directory, possibly changing the name or performing other operations
like compression in the process.
- CopyFiles() - Constructor for class CopyFiles
-
- CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.file.copy.method
-
A method used for copying files (e.g.
- CopyFilesMethod() - Constructor for class CopyFilesMethod
-
- CopyFilesNaming<T> - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
How an output name (and path) is selected for an input file when copying.
- CopyFilesNaming() - Constructor for class CopyFilesNaming
-
- CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
- CopyFilesNamingOne() - Constructor for class CopyFilesNamingOne
-
- CopyFilesNamingWithoutSharedState - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Base class for implementations of
CopyFilesNaming where each file is copied independently
of the others.
- CopyFilesNamingWithoutSharedState() - Constructor for class CopyFilesNamingWithoutSharedState
-
- copyFrom(int, int, ResultsVector, int) - Method in class ResultsVector
-
Copies a contiguous subset of results from another vector
- copyFrom(VoxelsWrapper, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source (of any type) to voxels of type T.
- copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
- copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
- copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
- copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.
- copyInit(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define AND initializes
- copyObjectsFrom(NamedProvider<ObjectCollection>) - Method in class ImageInitialization
-
- copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class DisplayStack
-
Copies pixels on a particular channel to an output buffer
- copyProvider(Class<?>, NamedProviderStore<T>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define AND initializes as a provider
- copyStacksFrom(NamedProvider<Stack>) - Method in class ImageInitialization
-
- copyTo(NameValueSet<Feature<T>>) - Method in class NamedFeatureStore
-
- copyTo(SharedObjects) - Method in interface ExportSharedObjects
-
Adds any exported shared-objects to sharedObjects.
- copyTo(SharedObjects) - Method in class MultiInput
-
- copyTo(SharedObjects) - Method in class FromCSVInput
-
- copyToDirectory(File) - Method in class TestLoader
-
Copies all the data in the test-data folder (recursively), preserving file-dates
- copyToDirectory(String[], File) - Method in class TestLoader
-
Copies specific subdirectories from the test-data folder (recursively), preserving file-dates
- copyToDuplicate(NameValueSet<Feature<T>>) - Method in class NamedFeatureStore
-
- copyVoxelsTo(BoundingBox, VoxelsWrapper, BoundingBox) - Method in class VoxelsWrapper
-
- copyVoxelsTo(ObjectMask, VoxelsWrapper, BoundingBox) - Method in class VoxelsWrapper
-
- copyWithoutInit(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define WITHOUT doing any initialization
- cornerMin() - Method in class BoundedVoxels
-
- cornerMin() - Method in class BoundingBox
-
The bottom-left corner of the bounding box.
- correctedEndIndex(int) - Method in class IndexRange
-
The end-index, corrected so that it is no longer negative.
- correctedStartIndex(int) - Method in class IndexRange
-
The start-index, corrected so that it is no longer negative.
- CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment
-
Stores costs between all possible pairings between elements from two lists.
- CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
- CostOverlapWithinMidpointDistance() - Constructor for class CostOverlapWithinMidpointDistance
-
- Count - Class in org.anchoranalysis.feature.bean.results
-
The number of the results from a particular feature.
- Count() - Constructor for class Count
-
- count() - Method in class PredicateAtCorner
-
- count() - Method in class PredicateImplementation
-
- count() - Method in interface VoxelsPredicate
-
Counts the number of values satisfying the predicate - across all voxels.
- count(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>) - Method in class CountIntersectingVoxels
-
- Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
Counts the number of items in a histogram (posssibly in relation to a threshold: above, below
etc.)
- Count() - Constructor for class Count
-
- countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded
-
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxels
that match a predicate.
- countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded
-
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask and match a predicate.
- CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- CountEqual() - Constructor for class CountEqual
-
- Counter - Class in org.anchoranalysis.math.arithmetic
-
A simple counter that increments
- Counter() - Constructor for class Counter
-
- countForObject(ObjectMask) - Method in class PredicateAtCorner
-
- countForObject(ObjectMask) - Method in class PredicateImplementation
-
- countForObject(ObjectMask) - Method in interface VoxelsPredicate
-
Counts the number of values satisfying the predicate - but restricted to voxels corresponding
to on in an object-mask.
- countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class CountVoxelsIntersectingObjects
-
Counts the number of intersecting-voxels between two object-masks.
- countIntersectingVoxels(ObjectMask) - Method in class ObjectCollection
-
- countIntersectingVoxels(ObjectMask) - Method in class ObjectMask
-
Counts the number of intersecting-voxels between two object-masks.
- CountIntersectingVoxels - Class in org.anchoranalysis.mpp.overlap
-
Counts the number of intersecting-pixels where bytes are encoded as region memberships
- CountIntersectingVoxels(byte) - Constructor for class CountIntersectingVoxels
-
- CountIntersectingVoxels(PredicateRegionMembership) - Constructor for class CountIntersectingVoxels
-
- countIntersectingVoxels() - Method in class MaxIntensityProjectionPair
-
- CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count
-
Base class for kernels that return a count (positive integer) for every voxel.
- CountKernel() - Constructor for class CountKernel
-
- CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count
-
For every voxel on the outline, count all neighbors that are adjacent.
- CountKernelNeighborhood() - Constructor for class CountKernelNeighborhood
-
- CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count
-
The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an
ObjectMask.
- CountKernelNeighborhoodMask(ObjectMask) - Constructor for class CountKernelNeighborhoodMask
-
Create with object-mask.
- countMasked(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, byte) - Method in class CountIntersectingVoxels
-
- countOff() - Method in class BinaryVoxels
-
- countOn() - Method in class BinaryVoxels
-
- countThreshold(RelationToThreshold) - Method in interface VoxelStatistics
-
- countThreshold(RelationToThreshold) - Method in class VoxelStatisticsCombined
-
- countThreshold(RelationToThreshold) - Method in class VoxelStatisticsFromHistogram
-
- countThreshold(RelationToValue, double) - Method in class Histogram
-
- CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- CoupledManifests - Class in org.anchoranalysis.plugin.io.manifest
-
- CoupledManifests(DeserializedManifest, int, Logger) - Constructor for class CoupledManifests
-
- CoupledManifests(Manifest, DeserializedManifest, Logger) - Constructor for class CoupledManifests
-
- CoupledManifestsInputManager - Class in org.anchoranalysis.plugin.io.bean.input.manifest
-
- CoupledManifestsInputManager() - Constructor for class CoupledManifestsInputManager
-
- create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class CostMatrix
-
Creates by calculating the cost between elements.
- create(Provider<T>) - Static method in class OptionalFactory
-
Creates from a provider if non-null.
- create(boolean, Supplier<T>) - Static method in class OptionalFactory
-
Creates only if a boolean flag is true, otherwise returns Optional.empty().
- create(String) - Static method in class OptionalFactory
-
Creates Optional.empty() for an empty string, or otherwise Optional.of().
- create() - Method in interface Provider
-
- create() - Method in class ProviderHolder
-
- create() - Method in class DictionaryProviderReference
-
- create() - Method in class RandomNumberGeneratorBean
-
- create() - Method in class EqualToBean
-
- create() - Method in class GreaterThanBean
-
- create() - Method in class GreaterThanEqualToBean
-
- create() - Method in class LessThanBean
-
- create() - Method in class LessThanEqualToBean
-
- create() - Method in class RelationBean
-
- create() - Method in class StringMap
-
- create(List<T>) - Method in interface CreateFromList
-
- create(boolean) - Method in interface ConcurrentModelPool.CreateModelForPool
-
Creates a model
- create(String) - Static method in class OptionalUtilities
-
Creates an Optional from a string that might be empty or null
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class OnlyIf
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class SwitchDetailedLogging
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToConsole
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToMultiple
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFile
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFileOnlyIfFailure
-
- create() - Method in class Define
-
- create() - Method in class DefinedNamed
-
- create() - Method in class DefineSingle
-
- create() - Method in class ListSequence
-
- create() - Method in class ParametersAsFeatures
-
- create() - Method in class PrependName
-
- create() - Method in class SelectFromShared
-
- create() - Method in class FeatureProviderDefine
-
- create() - Method in class FeatureProviderReference
-
- create(Class<? extends FeatureInput>) - Method in interface CacheCreator
-
- create(FeatureCSVMetadata, Outputter) - Static method in class FeatureCSVWriter
-
- create(Optional<String>, String) - Static method in class MultiNameFactory
-
Creates either a multi-name that is either has a single part or a double part.
- create(Class<? extends FeatureInput>) - Method in class HorizontalCacheCreator
-
- create(SharedObjects) - Static method in class FeaturesInitialization
-
- create(Logger, Path) - Static method in class FeaturesInitialization
-
Creates empty params
- create() - Method in class ImgLib2Lanczos
-
- create() - Method in class ImgLib2Linear
-
- create() - Method in class InterpolatorBean
-
- create() - Method in class None
-
- create() - Method in class ChannelProviderBinary
-
- create() - Method in class ChannelProviderTernary
-
- create() - Method in class ChannelProviderUnary
-
- create() - Method in class HistogramProviderUnary
-
- create() - Method in class MaskProviderUnary
-
- create() - Method in class ObjectCollectionProviderUnary
-
- create() - Method in class ArrangeRaster
-
- create() - Method in class StackProviderUnary
-
- create(Stack) - Static method in class BufferedImageFactory
-
- create(BufferedImage) - Static method in class CreateStackFromBufferedImage
-
- create(Dimensions, VoxelDataType) - Method in class ChannelFactory
-
Creates an empty initialized channel for a particular data-type
- create(Voxels<?>) - Method in class ChannelFactory
-
- create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactory
-
- create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactorySingleType
-
- create(String) - Static method in class ImageSizeSuggestionFactory
-
Creates a suggestion for how to resize an image.
- create(List<Point3i>) - Static method in class SingleObjectFromPointsFactory
-
- create(VoxelsWrapper, Optional<ObjectMask>) - Static method in class HistogramFromObjectsFactory
-
- create(Channel) - Static method in class HistogramFromObjectsFactory
-
- create(Channel, Mask) - Static method in class HistogramFromObjectsFactory
-
- create(Channel, ObjectMask) - Static method in class HistogramFromObjectsFactory
-
- create(Channel, ObjectCollection) - Static method in class HistogramFromObjectsFactory
-
- create(Map<Integer, T>, UnaryOperator<T>) - Method in class DecodeLabels
-
Creates a map of elements to other elements that are labelled with unique integers
(sequentially increasing) in voxels.
- create(int) - Method in class DecodeLabels
-
Creates a list of elements from voxels that are labelled with unique integers (sequentially
increasing)
- create(Channel) - Static method in class DisplayStack
-
- create(Stack) - Static method in class DisplayStack
-
- create(RGBStack) - Static method in class DisplayStack
-
- create(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class InitializationFactory
-
- create() - Method in class GenerateString
-
- create() - Method in class TileWithLabels
-
- create(InputOutputContext) - Static method in class ImageInitializationFactory
-
- create(InputOutputContext, Optional<ImageSizeSuggestion>) - Static method in class ImageInitializationFactory
-
- create() - Static method in class RasterDirectoryObjectsGenerator
-
- create(SliceBufferIndex<T>, VoxelDataType) - Method in class VoxelsFactory
-
- create(Extent, VoxelDataType) - Method in class VoxelsFactory
-
- create(SliceBufferIndex<T>) - Method in interface VoxelsFactoryTypeBound
-
- create(ObjectCollection, Extent, boolean, boolean) - Static method in class NeighborGraph
-
Create the graph with object-masks as vertices, where edges represent the number of
intersecting voxels between objects.
- create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class NeighborGraph
-
- create(ObjectCollection) - Static method in class IntersectingObjects
-
- create(VoxelBuffer<?>) - Static method in class HistogramFactory
-
- create(VoxelsWrapper) - Static method in class HistogramFactory
-
- create(IFormatReader, VoxelDataType, int) - Static method in class ConvertToFactory
-
- create(Path) - Static method in class CSVWriter
-
Creates and starts a CSVWriter (it's always allowed, so will never return null)
- create(String, Optional<ManifestDescription>, OutputterChecked, String) - Static method in class TextFileOutputter
-
- create() - Method in class ReadFromFile
-
- create(InputManagerParams) - Method in class FilesProvider
-
Creates or provides a collection of files.
- create(InputManagerParams) - Method in class FilesProviderUnary
-
- create(InputManagerParams) - Method in class FilesProviderWithDirectory
-
- create(InputManagerParams) - Method in class SpecificPathList
-
- create() - Method in class FilePathProviderReference
-
- create() - Method in class FromFiles
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class AddToDefaults
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class IgnoreUnderscorePrefixUnless
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class NoneExcept
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class OutputEnabledRules
-
Creates rules for determining whether an output is enabled or disabled.
- create(Optional<MultiLevelOutputEnabled>) - Method in class Permissive
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class PermissiveExcept
-
- create(CommandLine, Path, Path, Path) - Static method in class ExperimentExecutorFactory
-
Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR
accepts a path passed as the first command-line argument
- create() - Method in class MarkEllipseFactory
-
- create() - Method in class MarkEllipsoidFactory
-
- create() - Method in class MarkFactory
-
- create() - Method in class MarkPointListFactory
-
- create() - Method in class EnergySchemeCreator
-
- create() - Method in class EnergySchemeCreatorByElement
-
- create(EnergyStackWithoutParams) - Method in class DictionaryForImageCreator
-
- create(int) - Method in interface VoxelPartitionFactory
-
- create(int) - Method in class VoxelPartitonFactoryHistogram
-
- create(ImageInitialization, SharedObjects) - Static method in class PointsInitialization
-
- create(Optional<? extends ExportSharedObjects>, InitializationContext, Optional<Define>) - Static method in class MarksInitializationFactory
-
- create(List<Point3d>) - Static method in class PointListFactory
-
- create(List<Point3d>, int) - Static method in class PointListFactory
-
- create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class PxlMarkMemoFactory
-
- create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class VoxelizedMarkFactory
-
- create(Mark) - Method in class ProposerContext
-
- create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class Plot
-
Creates a graph
- create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class LinePlot
-
- create(InputManagerParams) - Method in class FromAnnotations
-
- create() - Method in class FromDimensionsBase
-
- create() - Method in class FromInput
-
- create() - Method in class FromStack
-
- create() - Method in class FromMaskBase
-
- create() - Method in class Reference
-
- create() - Method in class ScoreVoxels
-
- create() - Method in class Concatenate
-
- create() - Method in class GenerateToMatchObjects
-
- create() - Method in class FromChannel
-
- create() - Method in class GuessDimensions
-
- create() - Method in class SpecifyDimensions
-
- create() - Method in class FromChannel
-
- create() - Method in class Reference
-
- create() - Method in class FromStackChannel
-
- create() - Method in class FromChannelBase
-
- create() - Method in class FromDimensionsBase
-
- create() - Method in class Reference
-
- create() - Method in class Concatenate
-
- create() - Method in class ConnectedComponentsFromMask
-
- create() - Method in class Empty
-
- create() - Method in class IfParamEqual
-
- create() - Method in class FromMask
-
- create() - Method in class MergeTwoCollectionsItemwise
-
- create() - Method in class Permute
-
- create() - Method in class Reference
-
- create() - Method in class ReferenceOrElse
-
- create() - Method in class SegmentStack
-
- create() - Method in class WithChannelBase
-
- create() - Method in class ColoredBase
-
- create() - Method in class ThreeChannels
-
- create() - Method in class Concatenate
-
- create() - Method in class FromChannelOrMask
-
- create() - Method in class FromInput
-
- create() - Method in class PlotHistogram
-
- create() - Method in class Reference
-
- create() - Method in class DeriveFromPair
-
- create() - Method in class FeatureListProviderAggregatePair
-
- create() - Method in class PermuteFeatureBase
-
- create() - Method in interface PermuteFirstSecondOrder.CreateFirstSecondOrder
-
- create() - Method in class InterpolatorBeanImageJ
-
- create(InputManagerParams) - Method in class Combine
-
- create(InputManagerParams) - Method in class Rooted
-
- create() - Method in class FeatureListProviderLDAClassifier
-
- create() - Method in class FeatureListProviderSVMClassifier
-
- create() - Method in class MarkBoundsDefine
-
- create() - Method in class MarkBoundsReference
-
- create() - Method in class FromMarks
-
- create() - Method in class CreateNew
-
- create() - Method in class FromSingleMark
-
- create() - Method in class PointsFromObjects
-
- create() - Method in class Reference
-
- create() - Method in class ReferenceOrEmpty
-
- create() - Method in class ScaleXY
-
- create() - Method in class CreateEllipse
-
- create() - Method in class RequireFeatureRelationThreshold
-
- create() - Method in class RetrieveSingleMarkOnly
-
- create() - Method in class HOGDescriptor
-
- create() - Method in class FitPointsFromObjects
-
- create(InputManagerParams) - Method in class ExperimentResultsExperimentStructure
-
- create() - Method in class RotationMatrixFactory
-
- create() - Static method in class ConstantsInListFixture
-
creates a feature-list associated with the fixture
- createAddCriteria() - Method in class EnergySchemeWithSharedFeatures
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceFirstAndSecond
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceRatioFirstAndSecond
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class SubtractReducedFromMerged
-
- createAndStartSession() - Method in class ReportFeatureEvaluator
-
- createArguments(CommandLine) - Method in class LauncherConfig
-
- createAscending() - Static method in class HistogramFixture
-
a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count
5, value 100 has count 100 etc.)
- createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class AssignmentObjectFactory
-
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class AnnotationComparisonAssigner
-
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class FeatureCostAssigner
-
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class MaskIntersectionAssigner
-
- createAsStack() - Method in class ChannelProvider
-
- createAsStack() - Method in class MaskProvider
-
- createAsStack() - Method in class StackProvider
-
- createAsStack() - Method in interface ProviderAsStack
-
Creates from the image-bean in the form of a stack
- createAxisArray() - Method in class GradientBaseAddSum
-
- createAxisArray() - Method in class GradientForAxis
-
- createAxisArray() - Method in class GradientXY
-
- createBackground(NamedProviderStore<Stack>, String) - Static method in class BackgroundCreator
-
- createBean(Class, BeanDeclaration, Object) - Method in class DefineFactory
-
- createBean(Class<?>, BeanDeclaration, Object) - Method in class AnchorDefaultBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IncludeBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IncludeListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IndirectlyFromListBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class ListBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class ReplacePropertyBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class StringListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class StringSetFactory
-
- createBeanInstance(Class<?>, BeanDeclaration) - Method in class AnchorDefaultBeanFactory
-
- createBetweenTwoPoints(Point3d, Point3d) - Static method in class DirectionVector
-
- createBetweenTwoPoints(Point3i, Point3i) - Static method in class DirectionVector
-
- createBounded(BoundingBox) - Method in interface VoxelsFactoryTypeBound
-
Creates and initializes voxels that correspond to a particular bounding-box region.
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in interface ArrangeStack
-
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Overlay
-
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Single
-
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Tile
-
- createBufferedImage() - Method in class DisplayStack
-
- createBufferedImage(int, int) - Method in class PlotInstance
-
- createBufferedImageBBox(BoundingBox) - Method in class DisplayStack
-
- createBuilderWithDefaultErrorHandler() - Static method in class XMLUtilities
-
Creates a document-builder with default error-handling
- createByte() - Method in class Mask
-
- createByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createByte(Voxels<UnsignedByteBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createByte() - Method in class BinaryValues
-
- createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class DerivedObject
-
- createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class Erode
-
- createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class Shell
-
- createCalculator(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class MergedPairsFeatures
-
- createChannel(int, boolean) - Method in class DisplayStack
-
- createChannel() - Method in class CheckMarkWithMask
-
- createChannelDuplicate(int) - Method in class DisplayStack
-
- createChannelDuplicateForBoundingBox(int, BoundingBox) - Method in class DisplayStack
-
- createChannelsForSeries(int, Progress) - Method in class NamedChannelsInput
-
- createChart(DefaultCategoryDataset, String, Optional<AxisLimits>) - Method in class BarPlot
-
Creates a chart
- createChart(DefaultBoxAndWhiskerCategoryDataset, String, Optional<AxisLimits>) - Method in class BoxPlot
-
- createChart(XYDataset, String, Optional<AxisLimits>) - Method in class LinePlot
-
Creates a chart
- createChart(S, String, Optional<AxisLimits>) - Method in class PlotIndexBase
-
- createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class LevelResultCollectionFactory
-
- createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
-
- createColors(int) - Method in class ColorPool
-
- createCombinedException(String, Throwable) - Method in exception AnchorCombinableException
-
- CreateCombinedStack - Class in org.anchoranalysis.image.bean.nonbean.init
-
- createConverter() - Method in class ConvertChannelTo
-
- createConverter() - Method in class ConvertChannelToWithHistogram
-
- createConverter() - Method in class ToByteUpperLowerQuantileIntensity
-
- createConverter() - Method in class ScaleByMinMaxValue
-
- createConverter() - Method in class ScaleByParams
-
- createConverter() - Method in class ScaleByTypeToByte
-
- createConverter() - Method in class ToByte
-
- createCountKernelMask(ObjectMask) - Method in class TouchingVoxels
-
- createDataset(Iterator<T>) - Method in class LinePlot
-
- createDataset(Iterator<T>) - Method in class PlotIndexBase
-
- createDataset(Iterator<T>) - Method in class PlotIndexBaseCategorical
-
Creates a sample dataset
- createDefaultDataset() - Method in class BarPlot
-
- createDefaultDataset() - Method in class BoxPlot
-
- createDefaultDataset() - Method in class PlotIndexBaseCategorical
-
- createDelegate(Feature<T>) - Method in class PermuteDivideByParam
-
- createDelegate(Feature<T>) - Method in class PermuteFeatureSequenceInteger
-
- createDelegate(Feature<T>) - Method in class PermuteFirstSecondOrder
-
- createDescending() - Static method in class HistogramFixture
-
- createDescriptor(Extent) - Method in class HOGParameters
-
- createDesignMatrix(List<Point3f>) - Method in class LinearLeastSquaresViaNormalEquationBase
-
- createDictionary() - Method in class EnergyScheme
-
returns the associated
Dictionary or an empty set, if no params are associated with the energyScheme
- createDilatedObject(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class MorphologicalDilation
-
Dilates an object-mask, growing the bounding-box as necessary.
- createDim() - Method in class PointsFitterToMark
-
- createDimensions() - Method in class WithDimensionsBase
-
- createDims() - Method in class WithOptionalDimensionsBase
-
Returns the dimensions or null if none are provided
- createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, float) - Method in class DistanceTransform3D
-
- createDuplicatePxlMarkMemoList() - Method in class VoxelizedMarksWithEnergy
-
- CreateEllipse - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
- CreateEllipse() - Constructor for class CreateEllipse
-
- createEmptyInitialised(Dimensions) - Method in class ChannelFactorySingleType
-
- createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class ChannelFactory
-
Creates an empty initialized channel with discrete type with as minimal as needed data-type
to support a maximum value
- createEmptyMat(Extent, int) - Static method in class ConvertToMat
-
- createEmptyOff(Extent) - Static method in class BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off
(0).
- createEmptyOff(Extent, VoxelDataType) - Static method in class BinaryVoxelsFactory
-
Creates an empty binary-voxels of a particular data-type with all voxels initialized to OFF
(0)
- createEmptyOn(Extent) - Static method in class BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to ON (255)
- createEmptyStackFor(Dimensions) - Static method in class ObjectsAsRGBGenerator
-
- createEmptyUninitialised(Dimensions) - Method in class ChannelFactorySingleType
-
- CreateException - Exception in org.anchoranalysis.core.exception
-
- CreateException(String) - Constructor for exception CreateException
-
- CreateException(Throwable) - Constructor for exception CreateException
-
- CreateException(String, HasFriendlyErrorMessage) - Constructor for exception CreateException
-
- CreateException(String, AnchorCombinableException) - Constructor for exception CreateException
-
- createExperimentExecutor(CommandLine) - Method in class LauncherConfig
-
- createExperimentOutputter(Optional<String>, Manifest, RecordedOutputsWithRules, Optional<ImageFileFormat>, PathPrefixerContext, Optional<Logger>) - Method in class OutputManager
-
Creates an outputter for the experiment in general.
- createExperimentState() - Method in class SegmentIntoMarks
-
- createExperimentState() - Method in class SegmentWithMarkedPointProcess
-
- createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
-
- createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class FeatureValueIndividualEnergyGreaterThan
-
- createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class FeatureValueMarkGreaterEqualThan
-
- CreateFeatureInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session
-
- createFeatureList(String, TestLoader) - Static method in class FeaturesFromXmlFixture
-
- createFeatureNames() - Method in class NamedFeatureStore
-
- createFeatureNames() - Method in interface FeatureTableCalculator
-
Creates A list of names for each feature (columns of the table)
- createFeatureNames() - Method in class PairsTableCalculator
-
- createFeatureNames() - Method in class SingleTableCalculator
-
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class CombineObjectsForFeatures
-
Creates features that will be applied on the objects.
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class EachObjectIndependently
-
- createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class EachObjectIndependently
-
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class PairNeighbors
-
- createFeatureSession() - Method in class FeatureEvaluator
-
Creates session for evaluating feature optionally adding an energy-stack.
- createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class FeatureListEvaluator
-
Creates session for evaluating features.
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class AlwaysAllowed
-
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class CheckIfAllowed
-
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in interface Writer
-
The path to write a particular output to.
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class WriterRouterErrors
-
The path to write a particular output to.
- createFileOutputFor(String, FeedbackBeginParameters<VoxelizedMarksWithEnergy>, String) - Static method in class CSVReporterUtilities
-
- createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class EllipsoidFitHelper
-
- createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createFloat(Voxels<FloatBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createFloat(Extent) - Static method in class MaxIntensityProjection
-
- createFloat(Extent) - Static method in class MeanIntensityProjection
-
- createFloat(Voxels<FloatBuffer>) - Static method in class VoxelsExtracterFactory
-
- createForDirectoryPermissive(Path, boolean, Optional<Logger>) - Static method in class OutputterChecked
-
Creates, defaulting to a permissive output-manager in a particular directory.
- createForFeature(Feature<?>) - Method in interface CreateFeatureInput
-
- createForFeatures(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class SharedStateExportFeatures
-
Alternative static constructor that creates a shared-state from a list of named
feature-providers
- createForFeatures(NamedFeatureStore<T>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class SharedStateExportFeatures
-
Alternative static constructor that creates a shared-state from a feature-store
- createForFeatures(ResultsWriterOutputNames, FeatureTableCalculator<T>, LabelHeaders, InputOutputContext) - Static method in class SharedStateExportFeatures
-
Alternative static constructor that creates a shared-state from a feature-store
- createForSingle(AnchorBean<?>, String) - Static method in class PermutationSetterUtilities
-
Searches through a list of property fields to find one that matches the propertyName
- createForSubdirectory(String) - Method in class TestLoader
-
Creates a new test-loader for a subdirectory of the current test
- createForVoxelBuffer(VoxelBuffer<T>, Extent) - Method in interface VoxelsFactoryTypeBound
-
- createFrom(int, ObjectMask) - Method in interface DecodeLabels.CreateElementFromScaledObject
-
- createFrom(int, ObjectMask) - Method in interface AccessObjectMask
-
Creates an element of type T from an object-representation and index.
- createFromChannel(Channel) - Method in class ChannelProviderUnary
-
- createFromChannel(Channel) - Method in class AnisotropicDiffusion
-
- createFromChannel(Channel) - Method in class MinimumFilter
-
- createFromChannel(Channel) - Method in class Invert
-
- createFromChannel(Channel) - Method in class AssignFromDictionary
-
- createFromChannel(Channel) - Method in class AssignFromIntersectingObjects
-
- createFromChannel(Channel) - Method in class Convert
-
- createFromChannel(Channel) - Method in class ConvertWithHistogram
-
- createFromChannel(Channel) - Method in class Duplicate
-
- createFromChannel(Channel) - Method in class GradientBaseAddSum
-
- createFromChannel(Channel) - Method in class Sobel
-
- createFromChannel(Channel) - Method in class IfParamEquals
-
- createFromChannel(Channel) - Method in class Blur
-
- createFromChannel(Channel) - Method in class IfVoxelZero
-
- createFromChannel(Channel) - Method in class Median
-
- createFromChannel(Channel, ObjectCollection) - Method in class NormalizeDifferenceToMedian
-
- createFromChannel(Channel, ObjectCollection) - Method in class NormalizeObjectIntensity
-
- createFromChannel(Channel) - Method in class QuantileStretch
-
- createFromChannel(Channel) - Method in class ScaleXY
-
- createFromChannel(Channel) - Method in class UnaryWithMaskBase
-
- createFromChannel(Channel) - Method in class LevelPerObjectBase
-
- createFromChannel(Channel, ObjectCollection) - Method in class IdentifyObjects
-
- createFromChannel(Channel, ObjectCollection) - Method in class ScoreObjects
-
- createFromChannel(Channel) - Method in class ExtractCenterSlice
-
- createFromChannel(Channel) - Method in class ExtractSliceRange
-
- createFromChannel(Channel) - Method in class MaximumIntensityProjection
-
- createFromChannel(Channel) - Method in class MeanIntensityProjection
-
- createFromChannel(Channel) - Method in class UnaryWithObjectsBase
-
- createFromChannel(Channel, ObjectCollection) - Method in class UnaryWithObjectsBase
-
- createFromChannel(Channel) - Method in class UnaryWithValueBase
-
- createFromChannel(Channel) - Method in class SegmentChannel
-
- createFromChannel(Channel) - Method in class SegmentWithSeeds
-
- createFromChannel(Channel) - Method in class WithChannelBase
-
- createFromChannel(Channel, int) - Method in class BackgroundSubtractor
-
- createFromChannel(Channel) - Method in class EdgeFilterIJ
-
- createFromChannel(Channel) - Method in class GaussianBlur2D
-
- createFromChannel(Channel) - Method in class MedianFilter3D
-
- createFromChannel(Channel, int) - Method in class WithFilterBase
-
- createFromChannel(Channel) - Method in class WithRadiusBase
-
- createFromChannel(Channel, int) - Method in class WithRadiusBase
-
- createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantBase
-
- createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantConditionallyWriteBase
-
- createFromChannelWithConstant(Channel, double) - Method in class UnaryWithValueBase
-
- createFromDimensions(Dimensions) - Method in class DistanceTransformForEachObject3D
-
- createFromDimensions(Dimensions) - Method in class CreateNew
-
- createFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- createFromDimensions(Dimensions) - Method in class RepeatSlice
-
- createFromDimensions(Dimensions) - Method in class FromObjects
-
- createFromDimensions(Dimensions) - Method in class AllValuesOff
-
- createFromDimensions(Dimensions) - Method in class AllValuesOn
-
- createFromDimensions(Dimensions) - Method in class InsideBoxOn
-
- createFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- createFromExisting(InitializationContext, Optional<Define>, Optional<SharedObjects>, Optional<Dictionary>) - Static method in class MarksInitializationFactory
-
- createFromExplicitDirectory(String) - Static method in class TestLoader
-
Creates a new test-data loader using an explicit File path as root
- createFromExplicitDirectory(Path) - Static method in class TestLoader
-
Creates a new test-data loader using an explicit File path as root
- createFromFile(Path) - Method in class DeriveElementsFromSequencedDirectory
-
Creates an element of type T from a one particular file in the sequence.
- createFromFile(Path) - Method in class SequencedDirectoryDeserializer
-
- createFromFlag(boolean, T) - Static method in class OptionalUtilities
-
- createFromFlag(boolean, Supplier<T>) - Static method in class OptionalUtilities
-
- createFromFlagChecked(boolean, CheckedSupplier<T, E>) - Static method in class OptionalUtilities
-
Creates an
Optional from a boolean flag - where the supplier can thrown an exception
- createFromFlagOptional(boolean, Supplier<Optional<T>>) - Static method in class OptionalUtilities
-
- createFromGenerator(TransformingGenerator<BoundingBox, Stack>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates an extracted-object generator that draws an outline - with default color green and
flattened in Z.
- createFromHistogram(Histogram) - Method in class HistogramProviderUnary
-
- createFromHistogram(Histogram) - Method in class CutBelowThreshold
-
- createFromHistogram(Histogram) - Method in class GreaterThanThreshold
-
- CreateFromList<T> - Interface in org.anchoranalysis.bean.xml.factory
-
- createFromList(List<T>, Function<T, BoundingBox>) - Static method in class BoundedList
-
Creates for a list, minimally fitting a bounding-box around all elements
- createFromMarks(MarkCollection, KernelCalculationContext, Logger) - Static method in class VoxelizedMarksWithEnergyFactory
-
- createFromMask(Mask) - Method in class MaskProviderUnary
-
- createFromMask(Mask) - Method in class DistanceTransform3D
-
- createFromMask(Mask) - Method in class FromMask
-
- createFromMask(Mask) - Method in class FromMaskBase
-
- createFromMask(Mask) - Method in class CombineBase
-
- createFromMask(Mask) - Method in class Duplicate
-
- createFromMask(Mask) - Method in class Invert
-
- createFromMask(Mask) - Method in class MorphologicalOperatorBase
-
- createFromMask(Mask) - Method in class Outline
-
- createFromMask(Mask) - Method in class IfPredicateBase
-
- createFromMask(Mask) - Method in class FitBoxToOnVoxels
-
- createFromMask(Mask) - Method in class ScaleXY
-
- createFromMask(Mask) - Method in class FlattenZ
-
- createFromMask(Mask) - Method in class RepeatSlice
-
- createFromMask(Mask) - Method in class FillHoles
-
- createFromMask(Mask) - Method in class MorphologicalOperation
-
- createFromMask(Mask, Mask) - Method in class ConvexHull2D
-
- createFromMask(Mask, Mask) - Method in class ConvexHull3D
-
- createFromMask(Mask) - Method in class ConvexHullBase
-
- createFromMask(Mask, Mask) - Method in class ConvexHullBase
-
- createFromMaskedChannel(Channel, Mask) - Method in class SubtractMean
-
- createFromMaskedChannel(Channel, Mask) - Method in class AssignFromChannel
-
- createFromMaskedChannel(Channel, Mask) - Method in class AssignValue
-
- createFromMaskedChannel(Channel, Mask) - Method in class UnaryWithMaskBase
-
- createFromMaskedChannel(Channel, Mask) - Method in class ZeroOutsideMask
-
- createFromMavenWorkingDirectory() - Static method in class TestLoader
-
Creates a new test-data loader finding "src/test/resources" using the Maven working directory
- createFromMavenWorkingDirectory(String) - Static method in class TestLoader
-
Creates a new test-data loader finding "src/test/resources/PLUS_SOMETHING" using the Maven
working directory
- createFromNotObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class MaskFromObjects
-
We look for space NOT in the objects, and create channel to display it
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderUnary
-
- createFromObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class MaskFromObjects
-
We look for space IN objects, and create channel to display it
- createFromObjects(ObjectCollection) - Method in class AtIndex
-
- createFromObjects(ObjectCollection) - Method in class DecomposeIntoConnectedComponents
-
- createFromObjects(ObjectCollection) - Method in class RejectIfNotConnected
-
- createFromObjects(ObjectCollection) - Method in class Duplicate
-
- createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeature
-
- createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- createFromObjects(ObjectCollection) - Method in class SortByFeature
-
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class Filter
-
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class FilterByGroup
-
- createFromObjects(ObjectCollection) - Method in class IntersectsWithContainer
-
- createFromObjects(ObjectCollection) - Method in class Match
-
- createFromObjects(ObjectCollection) - Method in class NotInContainer
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderFilterBase
-
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class ObjectCollectionProviderFilterBase
-
- createFromObjects(ObjectCollection) - Method in class RemoveTouchingBorder
-
- createFromObjects(ObjectCollection) - Method in class AndObjectsWithMasks
-
- createFromObjects(ObjectCollection) - Method in class MergeGreedyToIncreaseObjectFeature
-
- createFromObjects(ObjectCollection) - Method in class MergeWithFeature
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderMorphological
-
- createFromObjects(ObjectCollection) - Method in class Scale
-
- createFromObjects(ObjectCollection, Channel) - Method in class BinarySegmentByObject
-
- createFromObjects(ObjectCollection, Channel) - Method in class SegmentChannelByObject
-
- createFromObjects(ObjectCollection) - Method in class ExtendInZ
-
- createFromObjects(ObjectCollection) - Method in class ExtendInZWithinContainer
-
- createFromObjects(ObjectCollection) - Method in class FlattenZ
-
- createFromObjects(ObjectCollection) - Method in class SliceAt
-
- createFromObjects(ObjectCollection) - Method in class RemoveIntersectingVoxels
-
- createFromObjects(ObjectCollection) - Method in class SplitByObjects
-
- createFromObjects(ObjectCollection) - Method in class SplitIntoSquares
-
- createFromObjects(ObjectCollection) - Method in class UnaryWithChannelBase
-
- createFromObjects(ObjectCollection, Channel) - Method in class UnaryWithChannelBase
-
- createFromObjects(ObjectCollection) - Method in class DrawLineAlongConvexHull
-
- createFromObjects(ObjectCollection) - Method in class FillHoles
-
- createFromObjects(ObjectCollection) - Method in class MergeSpatialClusters
-
- createFromObjects(ObjectCollection) - Method in class SplitContourAtSaddlePoints
-
- createFromOutputter(String, OutputterChecked) - Static method in class CSVWriter
-
Creates and starts a CSVWriter if it's allowed, otherwise returns
Optional.empty().
- createFromOutputterWithHeaders(String, OutputterChecked, Supplier<List<String>>, ErrorReporter) - Static method in class CSVWriter
-
- createFromOverlays(ColoredOverlayCollection, IdentifierGetter<Overlay>, IdentifierGetter<ObjectWithProperties>) - Static method in class ObjectDrawAttributesFactory
-
- createFromPath(Path) - Static method in class ObjectCollectionReader
-
Reads an object-collection from a path (or path prefix) trying different methods to read the
objects.
- createFromPathCached(CheckedSupplier<Path, OperationFailedException>) - Static method in class ObjectCollectionReader
-
- createFromSource(Channel) - Method in class AutoLocalThreshold
-
- createFromSource(Channel) - Method in class FromChannel
-
- createFromSource(Channel) - Method in class FromChannelBase
-
- createFromSource(Channel) - Method in class SegmentChannel
-
- createFromSource(Channel) - Method in class Threshold
-
- createFromStack(Stack) - Method in class StackProviderUnary
-
- createFromStack(ScaleableBackground, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with a stack as the background - and with default color green and
flattened in Z
- createFromStack(Optional<ScaleableBackground>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with maybe a stack as the background, or else an empty background - and
with default color green and flattened in Z
- createFromStack(Stack) - Method in class MontageSlices
-
- createFromStack(Stack) - Method in class ColorConverterBase
-
- createFromString(String) - Static method in class AxisTypeConverter
-
Maps a string of x, y, z (case ignored) to a corresponding axis type
- createFromThreeVectors(DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) - Static method in class RotationMatrix
-
- createFromTupleDuplicate(ReadableTuple3i) - Static method in class Extent
-
Createss an extent from a point (duplicating the point for internal use)
- createFromTupleReuse(ReadableTuple3i) - Static method in class Extent
-
Creates from a point that is reused internally (without duplication)
- createFromTwoMasks(Mask, Mask) - Method in class And
-
- createFromTwoMasks(Mask, Mask) - Method in class CombineBase
-
Creates masks from some combination of two masks
- createFromTwoMasks(Mask, Mask) - Method in class IfHighLow
-
- createFromTwoMasks(Mask, Mask) - Method in class Or
-
- createFromTwoMasks(Mask, Mask) - Method in class Xor
-
- createGenerator() - Method in class CombineRasterGenerator
-
- createGenerator() - Method in class TextStyle
-
Creates a generator, which produces a drawn string on an image when generated
- createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class BufferedImageFactory
-
- createGroupMap(ConsistentChannelChecker) - Method in class GroupedStackBase
-
Creates a map for the storing an aggregate-data-object for each group.
- createGroupMap(ConsistentChannelChecker) - Method in class ExportImageHistograms
-
- createGroupMap(ConsistentChannelChecker) - Method in class GroupedMeanChannelTask
-
- createHashMapToId() - Method in class MarkCollection
-
- createHeaders() - Method in class AnnotationGroup
-
- createHeaders() - Method in class AnnotationGroupObject
-
- createHeaders(boolean) - Method in class GenerateLabelHeadersForCSV
-
Creates the label-headers (the headers for columns not associated with features)
- createHistogramIgnoreZero(Channel, ObjectMask, boolean) - Static method in class HistogramFromObjectsFactory
-
- createIdArr() - Method in class MarkCollection
-
- createIdHashMap() - Method in class MarkCollection
-
- createImageDim() - Method in class ReportFeatureForMarks
-
- createImageFormat(String) - Static method in class FileFormatFactory
-
- createInitialization(InitializationContext, ExportSharedObjects) - Method in class DefineOutputter
-
- createInitialization(InitializationContext, Optional<SharedObjects>, Optional<Dictionary>) - Method in class DefineOutputter
-
- createInitializationContext() - Method in class InputBound
-
- createInitializationContext() - Method in class ParametersExperiment
-
- createInitialized(Extent) - Static method in class FromByte
-
- createInitialized(Extent) - Static method in class FromFloat
-
- createInitialized(Extent) - Static method in class FromInt
-
- createInitialized(Extent) - Static method in class FromShort
-
- createInitialized(Extent) - Method in interface VoxelsFactoryTypeBound
-
- createInputContext() - Method in class ExecutionArguments
-
Creates an input-context, reusing parameters from the experiment-execution
- createInputProcessContext(Optional<String>, InputOutputContext) - Method in class SharedStateExportFeatures
-
- createInputProcessContext(Optional<String>, InputOutputContext) - Method in class SharedStateSegmentInstance
-
- createInputsFromFiles(FilesProvider, InputManagerParams, Function<NamedFile, T>) - Method in class NamedFilesBase
-
Creates a list of inputs from a
FilesProvider which together with the
namer
can create the inputs.
- createInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createInt(Voxels<UnsignedIntBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createInt() - Method in class BinaryValuesByte
-
- createIntersectionComplement(ColoredOverlayCollection, ColoredOverlayCollection) - Static method in class ColoredOverlayCollection
-
- createInverted() - Method in class Mask
-
- createInverted() - Method in class BinaryValues
-
Inverts the values so OFF becomes ON, and vice-versa
- createKernel() - Method in class DilationContext
-
Creates a kernel for performing the dilation.
- createKernelFactoryNames() - Method in class KernelProposer
-
- createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class LabelObjects
-
Creates a channel that contains a unique integer (label) for each element's
object-representation.
- createList(int) - Method in class ColorScheme
-
Creates a list of colors of particular size.
- createList(int) - Method in class ColorSchemeUnary
-
- createList(int) - Method in class FromList
-
- createList(int) - Method in class FromSingle
-
- createList(int) - Method in class HSB
-
- createList(int) - Method in class VeryBright
-
- createListChildFeatures() - Method in class Feature
-
Returns a list of Features that exist as bean-properties of this feature, either directly or
in lists.
- createListMembershipWithFlags() - Method in class RegionMap
-
- createManifestDescription() - Method in class AssignmentGenerator
-
- createManifestDescription() - Method in class ChannelGenerator
-
- createManifestDescription() - Method in class ObjectsAsGrayscaleGenerator
-
- createManifestDescription() - Method in class HDF5ObjectsGenerator
-
- createManifestDescription() - Method in class ObjectAsMaskGenerator
-
- createManifestDescription() - Method in class ObjectsAsRGBGenerator
-
- createManifestDescription() - Method in class DrawObjectOnStackGenerator
-
- createManifestDescription() - Method in class ExtractBoundingBoxAreaFromStackGenerator
-
- createManifestDescription() - Method in class RasterGenerator
-
- createManifestDescription() - Method in class RasterGeneratorDelegateToDisplayStack
-
- createManifestDescription() - Method in class RasterGeneratorDelegateToRaster
-
- createManifestDescription() - Method in class RGBTimeSeriesGenerator
-
- createManifestDescription() - Method in class StackGenerator
-
- createManifestDescription(String) - Static method in class CollectionGenerator
-
- createManifestDescription() - Method in class DictionaryGenerator
-
- createManifestDescription() - Method in class SerializedGenerator
-
- createManifestDescription() - Method in class SingleFileTypeGenerator
-
- createManifestDescription() - Method in class SingleFileTypeGeneratorBridge
-
- createManifestDescription() - Method in class CSVGenerator
-
- createManifestDescription() - Method in class StringGenerator
-
- createManifestDescription() - Method in class MarksAsUniqueValueGenerator
-
- createManifestDescription() - Method in class MarksGeneratorBase
-
- createMap(OpenedImageFile) - Method in class ChannelMap
-
- createMap(OpenedImageFile) - Method in class Autoname
-
- createMap(OpenedImageFile) - Method in class FromEntries
-
- createMap(OpenedImageFile) - Method in class FromMetadata
-
- createMap(OpenedImageFile) - Method in class SingleChannel
-
- createMapToIndex() - Method in class FeatureNameList
-
Creates a map from the feature-names to their indices in the list
- createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class EllipsoidFactory
-
Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an
object-mask
- createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class EllipsoidFactory
-
- createMarkFromPoint(Point3i, int, boolean) - Static method in class MarkConicFactory
-
- createMarkFromPoint(Point3d, int, boolean) - Static method in class MarkConicFactory
-
- CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points
-
- CreateMarkFromPoints() - Constructor for class CreateMarkFromPoints
-
- createMarkFromPoints3f(List<Point3f>) - Static method in class PointListFactory
-
- createMarkFromPoints3i(List<Point3i>) - Static method in class PointListFactory
-
- createMaskOff(Dimensions) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to OFF
- createMaskOff(Dimensions, BinaryValues) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to OFF
- createMaskOn(Dimensions) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to ON
- createMaskOn(Dimensions, BinaryValues) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to ON
- createMatcherFile(Path, Optional<InputContextParams>) - Method in class MatchExtensions
-
- createMatcherFile(Path, Optional<InputContextParams>) - Method in class MatchGlob
-
- createMatcherFile(Path, Optional<InputContextParams>) - Method in class MatchRegularExpression
-
- createMatcherFile(Path, Optional<InputContextParams>) - Method in class PathMatcher
-
- createMaxIntensityBuffer(Extent) - Method in class Base
-
- createMeanIntensityBuffer(Extent) - Method in class Base
-
- createMerged(ColoredMarks) - Method in class ColoredMarks
-
- createMerged(MarkCollection) - Method in class MarkCollection
-
- createMerged(OverlayCollection) - Method in class OverlayCollection
-
- createMessageForDscr(String) - Method in exception BeanMisconfiguredXmlException
-
- createMessageForDscr(String) - Method in exception LocalisedBeanException
-
- createMessageForDscr(String) - Method in exception AnchorCombinableException
-
Creates a message for the exception from the description
- createMessageForDscr(String) - Method in exception NamedProviderGetException
-
- createMinusOne() - Method in class Extent
-
Creates a new Extent with each dimension decreased by one
- createMockFeatureWithCalculation() - Static method in class MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) which counts the
number of pixels in an object
- createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) with a result
calculated using a lambda
- createModelPool(ConcurrencyPlan) - Method in class SegmentStackIntoObjectsPooled
-
Creates the model pool (to be used by multiple threads)
- createModelPool(ConcurrencyPlan) - Method in class SegmentObjectsFromTensorFlowModel
-
- createModelPool(ConcurrencyPlan) - Method in class SuppressNonMaxima
-
- createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class NamedFeatureStoreFactory
-
Create a list of na
- createNamedFeatureProviders(String, TestLoader) - Static method in class FeaturesFromXmlFixture
-
- createNames() - Method in class FeatureList
-
- createNecessaryDirectories(Path) - Static method in class WriterUtilities
-
- CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
Creates a new channel with all values initialized to a constant (by default zero)
- CreateNew() - Constructor for class CreateNew
-
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
-
- CreateNew() - Constructor for class CreateNew
-
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
Creates a new empty collection of marks
- CreateNew() - Constructor for class CreateNew
-
- createNewDocument() - Static method in class XMLUtilities
-
Creates a new XML document.
- createNewMarkPos(Orientation2D, Ellipse, RandomNumberGenerator, Dimensions, double, double, boolean) - Static method in class MarkEllipseSimple
-
- createNext(int, int) - Method in interface TableItemArrangement.TableCreator
-
- createNullErrorReporter() - Static method in class LogUtilities
-
- createObject(Mask) - Static method in class SingleObjectFromChannelFactory
-
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class OverlayMark
-
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class OverlayObjectMask
-
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class Overlay
-
- createObjects(Path, Dimensions, boolean) - Method in class Comparer
-
- createObjects(Path, Dimensions, boolean) - Method in class AnnotationMarksComparer
-
- createObjects(Path, Dimensions, boolean) - Method in class MarksComparer
-
- createObjects(Path, Dimensions, boolean) - Method in class MaskComparer
-
- createObjects(Path, Dimensions, boolean) - Method in class ObjectComparer
-
- createObjects() - Method in class PointsFitterToMark
-
- createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class GeneratorBridge
-
Creates a bridge that maps ONE-TO-MANY from source to destination (i.e.
- createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class GeneratorBridge
-
Creates a bridge that maps ONE-TO-ONE from source to destination (i.e.
- createOrderProvider() - Method in class IncreasingIntegers
-
- createOrderProvider() - Method in class IncrementingIntegers
-
- createOrderProvider() - Method in class SequenceType
-
- createOrderProvider() - Method in class StringsWithoutOrder
-
- createOrReuse(Throwable) - Static method in exception InitException
-
- createOrReuse(T) - Method in class AlwaysNew
-
- createOrReuse(T) - Method in class CacheAndReuseStrategy
-
- createOrReuse(T) - Method in interface ReplaceStrategy
-
- createOrReuse(T) - Method in class ReuseSingletonStrategy
-
- createOutPathString() - Method in class AppendCsv
-
- createOutPathString() - Method in class AppendDictionary
-
- createOutPathString() - Method in class AppendFilePath
-
- createOutPathString() - Method in class AppendHistogram
-
- createOutPathString() - Method in class AppendMarks
-
- createOutPathString() - Method in class AppendObjects
-
- createOutPathString() - Method in class AppendStack
-
- createOutPathString() - Method in class AppendStackDirect
-
- createOutPathString() - Method in class FilePathAppendBase
-
- createPair(CreateCalculatorHelper, ImageInitialization, CacheTransferSourceCollection) - Method in class MergedPairsFeatures
-
- createPairsUnique() - Method in class RandomCollectionWithAddCriteria
-
- createPairsUnique() - Method in class EnergySavedPairs
-
- createParam(String, boolean) - Method in class PermuteFeatureSequenceInteger
-
- createParams() - Method in class TouchingVoxels
-
- createParams(boolean, boolean) - Method in class SurfaceNumberVoxelFaces
-
- createParams(boolean, boolean) - Method in class SurfaceNumberVoxels
-
- createParams(boolean, boolean) - Method in class SurfaceNumberVoxelsBase
-
- createPathDeriver(String, String) - Method in class FilePathAppendBase
-
Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups
The first group should correspond to top-level folder for the project The second group should
correspond to the unique name of the dataset.
- createPayloadCalculator() - Method in class MergePairs
-
- createPayloadCalculator() - Method in class MergeToIncreaseObjectFeature
-
- createPayloadCalculator() - Method in class MergeWithFeature
-
Determines the payload for any given or potential vertex
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeature
-
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureBase
-
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureSequenceInteger
-
- createPolicy() - Method in class ConvertBase
-
- createPrecalc(DrawOverlay, ObjectWithProperties, Dimensions) - Static method in class DrawOverlay
-
- createPrefixerContext() - Method in class ExecutionArguments
-
- createPrioritizer() - Method in class MergePairs
-
- createPrioritizer() - Method in class MergeToIncreaseObjectFeature
-
- createPrioritizer() - Method in class MergeWithFeature
-
Determines the priority (and selection criteria) used to allow merges between neighbors
- createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface Prioritizer
-
- createRadiiArray() - Method in class ConicBase
-
- createRadiiArray() - Method in class Ellipse
-
- createRadiiArray() - Method in class Ellipsoid
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class ConicBase
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipse
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipsoid
-
- createRasters(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, Logger, boolean) - Method in class MultipleComparer
-
- createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
- createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class BufferedImageFactory
-
- createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class ThreeChannels
-
- createRoot() - Static method in class ProposerFailureDescription
-
- createRotationMatrix() - Method in class Orientation
-
- createRotationMatrix() - Method in class Orientation2D
-
- createRotationMatrix() - Method in class Orientation3DEulerAngles
-
- createRotationMatrix() - Method in class OrientationAxisAngle
-
- createRotationMatrix() - Method in class OrientationIdentity
-
- createRotationMatrix() - Method in class OrientationRotationMatrix
-
- createRow(String[]) - Method in class ColumnDefinition
-
- createSameSize(ChannelProvider, String, Channel) - Static method in class DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing
channel
- createSameSize(MaskProvider, String, Channel) - Static method in class DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing
channel
- createScaledObject(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in class FromMask
-
- createScaledObject(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in interface ScaledOverlayCreator
-
Creates a scaled-version of the object to use as an overlay..
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class OverlayMark
-
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class OverlayObjectMask
-
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class Overlay
-
- createSecondLevelFromSet(StringSet) - Method in class AddToDefaults
-
- createSecondLevelFromSet(StringSet) - Method in class IgnoreUnderscorePrefixUnless
-
- createSecondLevelFromSet(StringSet) - Method in class NoneExcept
-
- createSecondLevelFromSet(StringSet) - Method in class OutputEnableRulesSpecify
-
- createSecondLevelFromSet(StringSet) - Method in class PermissiveExcept
-
- createSequence(VoxelDataType) - Method in class MultiBufferSized
-
- createSession() - Method in class ObjectCollectionProviderWithFeature
-
- createSet() - Method in class MarkCollection
-
- createSet() - Method in class ColoredOverlayCollection
-
- createSet() - Method in class OverlayCollection
-
- createSetter(AnchorBean<?>) - Method in class PermuteProperty
-
- createSetter(AnchorBean<?>) - Method in class PermutePropertyWithPath
-
- createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<U>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class FeatureSource
-
- createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class SingleRowPerInput
-
- createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class FromObjects
-
- createSharedStateJob(InputOutputContext) - Method in class ConvertImageFormat
-
Sets a new output-sequence for the series
- createSharedStateJob(InputOutputContext) - Method in class RasterTask
-
Creates a shared-state for the duration of a particular input-job
- createSharedStateJob(InputOutputContext) - Method in class MovieFromSlices
-
- createShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createShort(Voxels<UnsignedShortBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createSingle(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class MergedPairsFeatures
-
- createSingle(T, Function<T, BoundingBox>) - Static method in class BoundedList
-
Creates for a single element, using its current bounding-box.
- createSingleStack() - Method in class StackSeries
-
Puts all stacks in the series into a single image stack
- createStack(List<RGBStack>, ChannelFactorySingleType) - Method in class RasterArranger
-
- CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.bufferedimage
-
- createStackProvider(List<StackProviderWithLabel>, int, boolean, boolean, boolean) - Static method in class TileRasters
-
- createStackSequenceForSeries(int) - Method in interface StackSequenceInput
-
Creates a TimeSequence of stacks for a particular series number
- createStackSequenceForSeries(int) - Method in class ConvertNamedChannelsInputToStack
-
- createStatistics() - Method in interface Assignment
-
- createStatistics() - Method in class AssignmentMaskIntersection
-
- createStatistics() - Method in class AssignmentOverlapFromPairs
-
- createStatistics() - Method in class ConcurrentJobMonitor
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class MarkRegion
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class CenterSliceBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class GreatestAreaSlice
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class IndexedRegionBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class IndexedRegionBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class MaxNonZero
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class SelectSlicesWithIndexBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class Specific
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class Thresholded
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSlice
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceBase
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceWindow
-
- createStatisticsHeaderNames() - Method in interface Assignment
-
- createStatisticsHeaderNames() - Method in class AssignmentMaskIntersection
-
- createStatisticsHeaderNames() - Method in class AssignmentOverlapFromPairs
-
The headers needed to create statistics
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class AlwaysAllowed
-
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class CheckIfAllowed
-
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in interface Writer
-
Maybe creates a subdirectory for writing to.
- createSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class WriterRouterErrors
-
Maybe creates a subdirectory for writing to.
- createSubset(Collection<Integer>) - Method in class ObjectCollection
-
A subset of the collection identified by particular indices.
- createSubset(IntPredicate) - Method in class OverlayCollection
-
- createSubsetFromIDs(IntPredicate) - Method in class ColoredOverlayCollection
-
- createTransformerFactory() - Static method in class XMLUtilities
-
Creates a
TransformerFactory that ignores any DTDs in the document and disables
external entities (to prevent XXE attacks).
- createUninitialised(Dimensions, VoxelDataType) - Method in class ChannelFactory
-
- createUninitialized(Extent) - Static method in class FromByte
-
- createUninitialized(Extent) - Static method in class FromFloat
-
- createUninitialized(Extent) - Static method in class FromInt
-
- createUninitialized(Extent) - Static method in class FromShort
-
- createUninitialized(Extent) - Method in interface VoxelsFactoryTypeBound
-
- createUniqueNamesSorted() - Method in class FeatureNameList
-
- createUnsignedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class ObjectsFromConnectedComponentsFactory
-
- createUnsignedByte(Extent) - Static method in class MaxIntensityProjection
-
- createUnsignedByte(Extent) - Static method in class MeanIntensityProjection
-
- createUnsignedByte(Voxels<UnsignedByteBuffer>) - Static method in class VoxelsExtracterFactory
-
- createUnsignedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class ObjectsFromConnectedComponentsFactory
-
- createUnsignedInt(Extent) - Static method in class MaxIntensityProjection
-
- createUnsignedInt(Extent) - Static method in class MeanIntensityProjection
-
- createUnsignedInt(Voxels<UnsignedIntBuffer>) - Static method in class VoxelsExtracterFactory
-
- createUnsignedShort(Extent) - Static method in class MaxIntensityProjection
-
- createUnsignedShort(Extent) - Static method in class MeanIntensityProjection
-
- createUnsignedShort(Voxels<UnsignedShortBuffer>) - Static method in class VoxelsExtracterFactory
-
- createValues() - Method in class AnnotationGroup
-
- createValues() - Method in class AnnotationGroupObject
-
- createVector() - Method in class AxisAlignedUnitVector
-
- createVector() - Method in class DirectionVectorBean
-
Creates a vector in a particular direction
- createVector() - Method in class VectorInDirection
-
- createVector3d() - Method in class DirectionVector
-
- createWithConsoleFallback(OutputterChecked, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into
the console.
- createWithEmptyBackground(int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with an empty background - and with default color green and flattened
in Z
- createWithEmptyList() - Static method in class SpecificPathList
-
Factory method for creating the class with an empty list of paths
- createWithException(boolean, CheckedSupplier<T, E>) - Static method in class OptionalFactory
-
- createWithLogFallback(OutputterChecked, MessageLogger, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into a
log.
- createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
-
- createWithoutColor(ObjectCollection, IdentifierGetter<ObjectMask>) - Static method in class OverlayCollectionObjectFactory
-
- createWithoutStacks(InitializationContext) - Static method in class InitializationFactory
-
- createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteContext, Optional<WriteOperationRecorder>, Optional<MultiLevelRecordedOutputs>, boolean, Optional<Logger>) - Static method in class OutputterChecked
-
Creates a bound output-manager from an existing
OutputManager with a prefix.
- createWithRangeLimits(Iterator<T>, Optional<AxisLimits>) - Method in class PlotIndexBase
-
- createWithStacks(ProvidesStackInput, InitializationContext) - Static method in class InitializationFactory
-
- createWithXY(double) - Static method in class Resolution
-
Constructions with only XY resolution, identical in both dimensions.
- createWithXYAndZ(double, double) - Static method in class Resolution
-
Constructions with XY resolution and Z resolution.
- createWriter() - Method in class BioformatsWriter
-
Creates or gets an instance of IFormatWriter which dictates the file format to use
for writing.
- createWriter() - Method in class OMETiff
-
- createWriter() - Method in class OMEXML
-
- createWriter() - Method in class Tiff
-
- createWriter(OutputterChecked) - Method in class ExportReportFeatures
-
- cross(Vector3d, Vector3d) - Static method in class Vector3d
-
- CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular
-
- CSVGenerator(String) - Constructor for class CSVGenerator
-
- CSVReader - Class in org.anchoranalysis.io.input.csv
-
Reads a CSV File from the file-system.
- CSVReader(String, boolean) - Constructor for class CSVReader
-
- CSVReader(String, boolean, boolean) - Constructor for class CSVReader
-
- CSVReader.OpenedCSVFile - Class in org.anchoranalysis.io.input.csv
-
- CSVReaderByLine - Class in org.anchoranalysis.io.input.csv
-
Reads a CSV file line-by-line.
- CSVReaderByLine.ProcessCSVLine - Interface in org.anchoranalysis.io.input.csv
-
- CSVReaderException - Exception in org.anchoranalysis.io.input.csv
-
- CSVReaderException(String) - Constructor for exception CSVReaderException
-
- CSVReaderException(Throwable) - Constructor for exception CSVReaderException
-
- CSVReporterAggregated - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs statistics on current energy / kernel acceptance etc.
- CSVReporterAggregated() - Constructor for class CSVReporterAggregated
-
- CSVReporterBest - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs a CSV with statistics on the configuration/energy only the best
configuration state changes.
- CSVReporterBest() - Constructor for class CSVReporterBest
-
- CSVReporterUtilities - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- CSVRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
A row of the CSV File
- CSVRow(ColumnDefinition) - Constructor for class CSVRow
-
- csvString() - Method in class Histogram
-
- CSVWriter - Class in org.anchoranalysis.io.generator.tabular
-
- currentStateDescription() - Method in class ConcurrentJobMonitor
-
- currentTemperature() - Method in class AnnealScheme
-
- currentTemperature() - Method in class Geometry
-
- currentTemperature() - Method in class NoAnnealing
-
- customizeExperimentExecutor(ExperimentExecutor, CommandLine) - Method in class LauncherConfig
-
- CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the
threshold into the bin just below the threshold value
- CutBelowThreshold() - Constructor for class CutBelowThreshold
-
- CVFindContours - Class in org.anchoranalysis.plugin.opencv
-
Wrapper around Open CV's findContours function
- CVInit - Class in org.anchoranalysis.plugin.opencv
-
Provides for initialization of the JavaCPP bridge to OpenCV.
- GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
-
- GaussianBlur2D() - Constructor for class GaussianBlur2D
-
- GaussianCumulative<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
-
- GaussianCumulative() - Constructor for class GaussianCumulative
-
- GaussianSampler - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
Samples from a Gaussian distribution whose parameters are determined by a
Dictionary.
- GaussianSampler() - Constructor for class GaussianSampler
-
- generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawCroppedObjectsGenerator
-
- generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawObjectsGenerator
-
- generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface AddCriteria
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaEnergyPair
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaNever
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
-
- generateIntersectingObjects(int, int, boolean) - Static method in class IntersectingCircleObjectsFixture
-
Generates a number of circles that intersect and don't intersect
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter
-
- GenerateLabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature
-
Generates a list of header-names for columns unrelated to features (identifiers and groups)
- GenerateLabelHeadersForCSV(String[], Optional<String>) - Constructor for class GenerateLabelHeadersForCSV
-
- generateMasks(ObjectCollectionWithProperties) - Method in class DrawCroppedObjectsGenerator
-
- generateMasks(ObjectCollectionWithProperties) - Method in class DrawObjectsGenerator
-
- generateMasks(ObjectCollectionWithProperties) - Method in class ObjectsAsRGBGenerator
-
- generateNormal(double, double) - Method in interface RandomNumberGenerator
-
Generates a Gaussian (Normal) random variable with particular parameterization.
- generateNormal(double, double) - Method in class RandomNumberGeneratorMersenne
-
- generatePoisson(double) - Method in interface RandomNumberGenerator
-
Generates a Poisson random variable with particular parameterization.
- generatePoisson(double) - Method in class RandomNumberGeneratorMersenne
-
- generateProperties(Optional<Resolution>) - Method in class Ellipse
-
- generateProperties(Optional<Resolution>) - Method in class Ellipsoid
-
- generateProperties(Optional<Resolution>) - Method in class Mark
-
- generateProperties(Optional<Resolution>) - Method in class MarkWithPosition
-
- generateProperties(Optional<Resolution>) - Method in class OverlayMark
-
- generateProperties(Optional<Resolution>) - Method in class OverlayObjectMask
-
- generateProperties(Optional<Resolution>) - Method in class Overlay
-
- GenerateString - Class in org.anchoranalysis.image.io.bean.stack.combine
-
- GenerateString(String) - Constructor for class GenerateString
-
- GenerateString() - Constructor for class GenerateString
-
- GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider
-
Generates colors to match the size of an object-collection
- GenerateToMatchObjects() - Constructor for class GenerateToMatchObjects
-
- GenerateUniqueParameterization - Interface in org.anchoranalysis.bean
-
Objects that must implement well-defined equals() and hashCode() methods and also
generate a name uniquely identifying the class and all parameterization
- generator() - Static method in class ObjectCollectionWriter
-
- Generator<T> - Interface in org.anchoranalysis.io.generator
-
A class that writes a particular type of object(s) to the filesystem.
- GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator
-
Exposes a Generator<T> as if it was an Generator<S>.
- GeneratorOutputter - Class in org.anchoranalysis.image.io.stack.output.generator
-
Settings and methods for writing to the filesystem from a generator.
- Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
-
- Geometry() - Constructor for class Geometry
-
- Geometry(double, double) - Constructor for class Geometry
-
- get(Class<? extends T>) - Method in class BeanInstanceMap
-
- get() - Method in class CachedSupplier
-
- get(K) - Method in class LRUCache
-
- get(int) - Method in interface ColorIndex
-
- get(int) - Method in class ColorIndexModulo
-
- get(int) - Method in class ColorList
-
- get(int) - Method in class SingleColor
-
- get() - Method in class WithPriority
-
- get() - Method in interface CheckedSupplier
-
Applies a supplier like with Supplier.get().
- get() - Method in interface StoreSupplier
-
Gets the object being supplied to the store
- get(int) - Method in class BoundedIndexContainerFromList
-
- get(int) - Method in class BoundsFromRange
-
- get(int) - Method in class BoundedIndexContainerBridge
-
- get(int) - Method in class IntegerSequenceContaner
-
- get(int) - Method in class SingleContainer
-
- get(int) - Method in interface GetterFromIndex
-
- get(Progress) - Method in class CachedProgressingSupplier
-
- get(Progress) - Method in interface CheckedProgressingSupplier
-
- get() - Static method in class ProgressIgnore
-
- get(int) - Method in class FeatureList
-
- get() - Method in interface SessionInput
-
Returns the underlying feature-input (independent of the session)
- get(int) - Method in class FeatureNameList
-
- get(int) - Method in class ResultsVector
-
- get(int) - Method in class ResultsVectorList
-
- get() - Method in interface CacheSupplier
-
- get() - Method in class SessionInputSequential
-
- get(int) - Method in class NamedFeatureStore
-
- get(String) - Method in class NamedFeatureStore
-
- get(int) - Method in class BoundingBoxesOnPlane
-
- get(int, int) - Method in class TableItemArrangement
-
- get(int) - Method in class ObjectCollectionWithProperties
-
- get(int) - Method in class SeedCollection
-
- get(int) - Method in class ContiguousVoxelPath
-
- get(Progress) - Method in interface NamedStacksSupplier
-
- get(int) - Method in class TimeSequence
-
- get(String) - Method in class NamedEntries
-
- get(Progress) - Method in interface TimeSequenceSupplier
-
- get(int) - Method in class StackSeries
-
- get(VoxelDataType) - Method in class VoxelDataTypeFactoryMultiplexer
-
Multiplexes one of the factories according to data-type
- get(int) - Method in class ObjectCollection
-
- get(int) - Method in class VoxelsWrapperList
-
- get(int) - Method in interface DestinationChannelForIndex
-
- get() - Method in interface PathSupplier
-
- get(int) - Method in class DeriveElementsFromSequencedDirectory
-
- get() - Method in class FinderDictionary
-
- get() - Method in class FinderFileAsText
-
- get() - Method in class FinderSerializedObject
-
- get() - Method in interface SerializedObjectSupplier
-
- get(Optional<String>) - Method in class InputOutputContextSubdirectoryCache
-
Gets (from the cache if it's already there) a context for a subdirectory of given-name
- get() - Method in interface ElementSupplier
-
Gets/creates the element to be written.
- get() - Method in interface ElementWriterSupplier
-
- get(int) - Method in class RunningSumCollection
-
An individual item in the collection.
- get(int) - Method in class ImageMoments
-
- get(int) - Method in class MarksWithTotalEnergy
-
- get(int) - Method in class EnergySavedInd
-
- get(String) - Method in class EnergySchemeSet
-
- get(int) - Method in class MemoList
-
- get(int) - Method in class UpdatableMarksList
-
- get(int) - Method in class IndexByChannel
-
- get(String) - Method in interface MultiInputSubMap
-
Returns null if non-existent
- get(String) - Method in class OperationMap
-
- get(String) - Method in class StackWithMap
-
- get(int) - Method in class MarkCollection
-
- get(int) - Method in class WeightedKernelList
-
- get(int) - Method in class AggIDCounter
-
- get(int) - Method in class ColoredOverlayCollection
-
- get(int) - Method in class OverlayCollection
-
- get(T, int) - Method in interface GetForSeries
-
- get(String) - Method in class GroupedAnnotationLabels
-
- get(int) - Method in class ListWithThumbnails
-
- get() - Method in class PriorityQueueIndexRangeDownhill
-
- get(T) - Method in class FileLabelMap
-
- get() - Method in class DeserializedManifest
-
- get(String) - Method in class IndexedCSVRows
-
- get(String) - Method in class MapGroupToRow
-
- get() - Method in interface FeatureResultSupplier
-
- get(int) - Method in class BoundedList
-
Gets a particular element
- getAboveMaxValue() - Method in class RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- getAcceptAll() - Method in class Aggregator
-
- getAdd() - Method in class VisualizeOnBackground
-
- getAddCriteria() - Method in class RandomCollectionWithAddCriteria
-
- getAdditionalBackgrounds() - Method in class MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- getAdditionalChannels() - Method in class MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalChannels() - Method in class NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalPropertyPaths() - Method in class PermutePropertyWithPath
-
Additional property paths that are also changed, along with the main propertyPath *
- getAddSum() - Method in class GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- getAdjacentChannels() - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- getAfterPreoperation() - Method in class OverlappingObject
-
After pre-operation but before scaling
- getAggInterval() - Method in class ReporterInterval
-
- getAggIntervalLog10() - Method in class ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- getAggregateReceiver() - Method in class ReporterAggregate
-
- getAggregateReceiver() - Method in class ConsoleAggregatedReporter
-
- getAggregateReceiver() - Method in class CSVReporterAggregated
-
- getAggregateReceiver() - Method in class Log4JReporter
-
- getAggregateReceiver() - Method in class MemoryUsageReporter
-
- getAggregateReceiver() - Method in class OptimizationStepLogReporter
-
- getAggregateReceiver() - Method in class TextFile
-
- getAggregateTriggerBank() - Method in class FeedbackBeginParameters
-
- getAll() - Method in class MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our
calculations for the 'all' component
- getAllCacheNames() - Method in class CacheTransferSourceCollection
-
- getAllKernelFactories() - Method in class KernelProposer
-
- getAllowsChildren() - Method in class ErrorNodeImpl
-
- getAngle() - Method in class OrientationAxisAngle
-
Angle part of axis-angle orientation (in radians)
- getAngleDegrees() - Method in class Orientation2D
-
- getAngleDegrees() - Method in class AngleRotation
-
- getAngleRadians() - Method in class Orientation2D
-
- getAnnealScheme() - Method in class SimulatedAnnealing
-
- getAnnotations() - Method in class FromAnnotations
-
- getAnnotatorStrategy() - Method in class AnnotationInputManager
-
- getAppendChannels() - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- getAppendCSV() - Method in class FromCSVInputManager
-
- getAppendCsv() - Method in class MatchedAppendCsv
-
- getAppendDictionary() - Method in class MultiInputManager
-
- getAppendFilePath() - Method in class MultiInputManager
-
- getAppendHistogram() - Method in class MultiInputManager
-
- getAppendMarks() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotation() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotationAcceptedOnly() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotationRejectedOnly() - Method in class MultiInputManager
-
- getAppendObjects() - Method in class MultiInputManager
-
- getAppendStack() - Method in class MultiInputManager
-
- getArbitraryElement() - Method in interface NamedProvider
-
Gets one element of the provider (arbitrarily)
- getArrange() - Method in class ArrangeRaster
-
- getArrange() - Method in class Cell
-
- getArrange() - Method in class CombineRasterGenerator
-
- getAsBoolean() - Method in interface CheckedBooleanSupplier
-
Applies a supplier like with BooleanSupplier.getAsBoolean().
- getAsDouble(String) - Method in class Dictionary
-
Retrieves a value from the dictionary, and converts to a double.
- getAssigner() - Method in class CompareAnnotations
-
- getAssignMode() - Method in class SimulatedAnnealing
-
- getAssociatedElementRange() - Method in class MutableDirectory
-
- getAssociatedElementRange() - Method in interface SequencedDirectory
-
The associated element-range with ths folder.
- getAssociatedMark() - Method in class ErrorNodeImpl
-
- getAsString(String) - Method in class Dictionary
-
Retrieves a value from the dictionary as a
String.
- getAsSupplier(String) - Method in class NamedStacks
-
- getAttributes() - Method in class StackWriteOptions
-
The attributes of the particular stack to write.
- getAxis() - Method in class AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- getAxis() - Method in class OrientationAxisAngle
-
Axis part of axis-angle orientation (should be normalized)
- getAxis() - Method in class CenterOfGravity
-
- getAxis() - Method in class GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- getAxis() - Method in class ForSpecificAxis
-
- getAxis() - Method in class ArbitraryInsidePoint
-
- getAxis() - Method in class BoundingBoxAlongAxisBase
-
- getAxis() - Method in class GradientMeanForAxis
-
- getAxis() - Method in class PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- getAxis() - Method in class BoundingBoxExtent
-
- getAxisColor() - Method in class PlotColorScheme
-
- getAxisMax() - Method in class AxisLimits
-
- getAxisMin() - Method in class AxisLimits
-
- getBackground() - Method in class AnnotatorStrategy
-
- getBackground() - Method in class ObjectsAsRGBGenerator
-
A background image or dimensions to define an empty background.
- getBackground() - Method in class DualStack
-
The background
- getBackground() - Method in class ColoredBase
-
The background.
- getBackgroundChannelIndex() - Method in class OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- getBackgroundChannelName() - Method in class CompareAnnotations
-
- getBackgroundChannelProvider() - Method in class MorphologicalOperatorBase
-
- getBackgroundColor() - Method in class PlotColorScheme
-
- getBackgroundID() - Method in class VisualizeOnBackground
-
- getBackgroundStackMap() - Method in class AnnotationBackground
-
If non-null, maps underlying stack-name to a background
- getBackgroundStackName() - Method in class SegmentIntoMarks
-
- getBaseName() - Method in class FilenameSplitExtension
-
The part of the filename without an extension.
- getBeanExtension() - Method in class QuickMultiDatasetExperiment
-
- getBeanExtension() - Method in class QuickMultiDatasetStructuredExperiment
-
- getBeanName() - Method in class AnchorBean
-
A short-name identifying a bean (by default the name of the class associated with the bean).
- getBelowMinValue() - Method in class RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- getBest() - Method in class DualState
-
- getBest() - Method in class OptimizationStep
-
- getBestState() - Method in class Reporting
-
- getBinaryInputChannelID() - Method in class AddDistanceTransform
-
The ID of the binary input mask that determines the region of the watershed
- getBinarySgmn() - Method in class BinarySegmentByObject
-
- getBirthRepeats() - Method in class KernelReplace
-
- getBitsPerPixel() - Method in class ForceBitsPerPixel
-
- getBlockSize() - Method in class HOGParameters
-
The block-size as per OpenCV implementation (identical default-size)
- getBlockStride() - Method in class HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size)
- getBlue() - Method in class RGBColorBean
-
- getBlue() - Method in class RGBColor
-
- getBlue() - Method in class ThreeChannels
-
- getBorderWidth() - Method in class MontageSlices
-
Adds a border around each part of the montage
- getBoundRadius() - Method in class MarkWithPositionAndSingleRadius
-
- getBounds() - Method in class RandomOrientation
-
- getBoundType() - Method in class BoundChangeEvent
-
- getBridgeMatcher() - Method in class Bridge
-
Used to match each input-object to an intermediary-object
- getBundleSize() - Method in class ObjectSerializerPeriodicReporter
-
- getBundleSize() - Method in class VoxelizedMarksChangeReporter
-
- getCache() - Method in interface SessionInput
-
- getCache() - Method in class CacheAndReuseStrategy
-
- getCache() - Method in class SessionInputSequential
-
- getCacheNames() - Method in class CacheTransferSource
-
- getCacheSize() - Method in class RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- getCalculateLevel() - Method in class CalculateLevelOne
-
- getCalculateLevel() - Method in class ThresholderGlobal
-
- getCalculateLevel() - Method in class LevelPerObjectBase
-
Method to calculate the level for a particular object.
- getCalculateLevel() - Method in class GreaterThanThreshold
-
Calculates the level for the threshold
- getCalculateLevel() - Method in class LevelFromHistogram
-
- getCalculateLevel() - Method in class ThresholdHistogram
-
- getCalculateLevel() - Method in class CalculateLevelBase
-
- getCalculateLevelElse() - Method in class CalculateLevelRelativeToThreshold
-
- getCalculator() - Method in class NamedFeatureCalculatorMulti
-
- getCellDefault() - Method in class Tile
-
- getCells() - Method in class Tile
-
- getCellSize() - Method in class HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size)
- getCenter() - Method in class SlidingBuffer
-
The buffer for the currently selected slice.
- getCenterPoint() - Method in class FitResult
-
- getCenterPointX() - Method in class EllipseStandardFormConverter
-
- getCenterPointY() - Method in class EllipseStandardFormConverter
-
- getChangedMarkIDArr() - Method in class KernelDescision
-
- getChangedMarkIDs() - Method in class Reporting
-
- getChannel(int) - Method in class EnergyStack
-
- getChannel(int) - Method in class EnergyStackWithoutParams
-
- getChannel() - Method in class ChannelProviderUnary
-
- getChannel(int) - Method in class Stack
-
- getChannel(int) - Method in class StackNotUniformSized
-
- getChannel(String, int, Progress) - Method in class ChannelFilter
-
- getChannel() - Method in class ChannelFilter
-
- getChannel(String, int, Progress) - Method in interface ChannelGetter
-
- getChannel(String, int, Progress) - Method in class NamedChannelsForSeriesConcatenate
-
- getChannel(String, int, Progress) - Method in class NamedChannelsForSeriesMap
-
- getChannel() - Method in class FromChannel
-
- getChannel() - Method in class FromChannel
-
- getChannel() - Method in class FromChannelBase
-
- getChannel() - Method in class IntensityGreaterEqualThan
-
- getChannel() - Method in class UnaryWithChannelBase
-
- getChannel() - Method in class WithChannelBase
-
- getChannel() - Method in class FromChannelOrMask
-
A channel that is provided to the stack.
- getChannel() - Method in class NamedChannel
-
- getChannel(String) - Method in class ChannelGetterForTimepoint
-
- getChannel1() - Method in class ChannelProviderBinary
-
- getChannel1() - Method in class ChannelProviderTernary
-
- getChannel2() - Method in class ChannelProviderBinary
-
- getChannel2() - Method in class ChannelProviderTernary
-
- getChannel3() - Method in class ChannelProviderTernary
-
- getChannelAssignFrom() - Method in class AssignFromChannel
-
- getChannelChecker() - Method in class GroupedSharedState
-
- getChannelConversionStyle() - Method in class ConvertImageFormat
-
To convert as RGB or independently or in another way
- getChannelConverter() - Method in class Convert
-
- getChannelConverter() - Method in class ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
- getChannelElse() - Method in class IfParamEquals
-
- getChannelFilter() - Method in class ConvertImageFormat
-
Optionally, includes only certain channels when converting.
- getChannelFirst() - Method in class Difference
-
Index of first channel
- getChannelGroupID() - Method in class RegularExpression
-
- getChannelID() - Method in class AddEdgeFilters
-
The ID of the channel that provides the input to the filter
- getChannelIfVoxelZero() - Method in class IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
- getChannelIndex() - Method in class FromStack
-
- getChannelIndex() - Method in class FromStackChannel
-
- getChannelIndex() - Method in class One
-
- getChannelIndex() - Method in class FileDetails
-
- getChannelIndex() - Method in class MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which
channel to use from the stack
- getChannelLookup() - Method in class NormalizeDifferenceToMedian
-
- getChannelMap() - Method in class NamedChannels
-
- getChannelMask() - Method in class ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the
histogram
- getChannelName() - Method in class ChannelFilter
-
- getChannelName() - Method in class SingleChannel
-
- getChannelName() - Method in class ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- getChannelNum() - Method in class SortedSetChannel
-
- getChannelOptional(String, int, Progress) - Method in interface NamedChannelsForSeries
-
Gets a channel if it exists, returning empty if it doesn't
- getChannelOptional(String, int, Progress) - Method in class NamedChannelsForSeriesConcatenate
-
- getChannelOptional(String, int, Progress) - Method in class NamedChannelsForSeriesMap
-
- getChannelSecond() - Method in class Difference
-
Index of second channel
- getChannelsExtra() - Method in class ScoreVoxels
-
- getChannelsPerByteArray() - Method in class ForceChannelsPerByteArray
-
- getChannelThreshold() - Method in class ThresholdAgainstChannel
-
- getChannelType() - Method in class ConsistentChannelChecker
-
- getChart() - Method in class PlotInstance
-
- getCheck() - Method in class Not
-
- getChecked() - Method in class Outputter
-
- getCheckMark() - Method in class FromObjects
-
- getCheckMark() - Method in class Check
-
- getCheckMark() - Method in class Check
-
- getCheckParsedFilePathBag() - Method in class GroupFiles
-
Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be
included.
- getChildAt(int) - Method in class ErrorNodeImpl
-
- getChildCount() - Method in class ErrorNodeImpl
-
- getClassifierProvider() - Method in class BinaryClassifierImageLabeller
-
- getClassLabelsPath() - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the class-labels file, a text file where each line specifies a class label in order, relative to the models/ directory in the Anchor distribution.
- getClassOfTarget() - Method in class ExtractFromParam
-
- getCode(int) - Method in class EncodedIntBuffer
-
- getCol(int) - Method in class TableItemArrangement
-
- getCol() - Method in class Cell
-
- getColForListIndex(int) - Method in class TableItemArrangement
-
- getCollection() - Method in class KernelDeath.MarkAnd
-
- getCollectionID() - Method in class ParamFromCollection
-
- getColor() - Method in class FromSingle
-
The single color to repeat.
- getColor(int) - Method in class ColoredOverlayCollection
-
- getColor() - Method in class AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- getColor() - Method in class ColoredMask
-
- getColorIDGetter() - Method in class ObjectDrawAttributes
-
Gets a color ID associated with the object
- getColorIndex() - Method in class ObjectDrawAttributes
-
Colors for a given index
- getColorList() - Method in class ColoredMarks
-
- getColors() - Method in class ColorSchemeUnary
-
The delegate that creates the (unshuffled) list.
- getColors() - Method in class FromList
-
The list of colors to specify
- getColors() - Method in class ColoredOverlayCollection
-
- getColors() - Method in class ColoredBaseWithGenerator
-
Colors to use for drawing objects
- getColors() - Method in class ColoredObjectCollection
-
The colors in the collection.
- getColorScheme() - Method in class GenerateToMatchObjects
-
- getColorsUnpaired() - Method in class CompareAnnotations
-
- getColorUnselectedObjects() - Method in class OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- getColumnDefinition() - Method in class ExportObjectsFromCSV
-
Column definition for the CSV files
- getColumnGroup() - Method in class ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- getColumnID() - Method in class ColumnDefinition
-
Name of CSV column with the file identifier
- getColumns() - Method in class MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- getColumnUniquePixel() - Method in class ColumnDefinition
-
Name of CSV column with X coordinate of point for the first Object
- getCombine() - Method in class FromObjects
-
- getCombined() - Method in interface VoxelPartition
-
- getCombined() - Method in class VoxelPartitionHistogram
-
- getCommand() - Method in class MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- getCommandName() - Method in class HelpConfig
-
What the application command is described as in the help message e.g. anchor or
anchorGUI
- getComparerLeft() - Method in class AnnotationComparisonInputManager
-
- getComparerMultiplex(boolean) - Method in class AnnotationComparisonInput
-
- getComparerRight() - Method in class AnnotationComparisonInputManager
-
- getComparers() - Method in class AnnotationComparisonInput
-
- getCondition() - Method in class IfParamEquals
-
- getCondition() - Method in class IfKeyValueCondition
-
- getConfidence() - Method in class LabelledWithConfidence
-
- getConfidence() - Method in class WithConfidence
-
- getConfidenceThreshold() - Method in class ConditionallyMergeOverlappingObjects
-
The maximum difference in confidence for merging.
- getConnPoint() - Method in class ContiguousVoxelPath
-
- getConstant() - Method in class MaxWithConstant
-
- getContains() - Method in class DescriptiveNameContainsImageLabeller
-
- getContains() - Method in class FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- getContext() - Method in class SharedObjects
-
Logger and other common configuration
- getContext() - Method in class ParametersExperiment
-
- getContext() - Method in class OutputterChecked
-
General settings for writing outputs.
- getContext() - Method in class InputProcessContext
-
- getContextExperiment() - Method in class InputBound
-
The input-output context associated with the current experiment.
- getContextJob() - Method in class InputBound
-
The input-output context associated with the current job.
- getConvert() - Method in class ConvertWithHistogram
-
- getConverters() - Method in class DisplayStack
-
- getCopyFilesNaming() - Method in class CopyFilesNamingOne
-
- getCost(int, int) - Method in class CostMatrix
-
Gets the cost from an element from the first-list to an element from the second-list.
- getCost() - Method in class MergeStrategy
-
A cost of how undesirable (the higher the more undesirable) this merge is.
- getCosts() - Method in class AssignmentObjectFactory
-
- getCount() - Method in class Counter
-
- getCount() - Method in class RunningSum
-
The running count
- getCount(int) - Method in class Histogram
-
- getCount() - Method in class VarianceCalculator
-
- getCountThreshold() - Method in class SummarizerSplitMoreThan
-
If there are more than countThreshold elements, use summarizerGreaterThan,
else summarizerElse.
- getCountXY() - Method in class RunningSumPoint
-
The count for XY dimensions (guaranteed to always be the same
- getCountZ() - Method in class RunningSumPoint
-
- getCreateMark() - Method in class PointsFitter
-
- getCsvFeaturesAggregated() - Method in class ResultsWriterOutputNames
-
The CSV of aggregated feature-results, if enabled.
- getCsvFeaturesGroup() - Method in class ResultsWriterOutputNames
-
The CSV individually written for each group, if enabled.
- getCsvFeaturesNonAggregated() - Method in class ResultsWriterOutputNames
-
The CSV of non-aggregated feature-results
- getCsvFilePath() - Method in class FilterCsvColumn
-
- getCsvFilePath() - Method in class FromCSVInput
-
- getCurrent() - Method in class DualState
-
- getCurrent() - Method in class OptimizationStep
-
- getCurrentTemp() - Method in class Geometry
-
- getCustomName() - Method in class Feature
-
An optional additional name that be associated with the feature (defaults to an empty string)
- getDatasetName() - Method in class ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- getDatasets() - Method in class QuickMultiDatasetExperiment
-
- getDatasets() - Method in class QuickMultiDatasetStructuredExperiment
-
- getDatasetSpecific() - Method in class QuickMultiDatasetExperiment
-
- getDatasetSpecific() - Method in class QuickMultiDatasetStructuredExperiment
-
- getDatasetSuffix() - Method in class FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- getDatasetVersion() - Method in class ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- getDebugModeParams() - Method in class InputManagerParams
-
- getDebugModeParams() - Method in class InputContextParams
-
Parameters for debug-mode (only defined if we are in debug mode)
- getDecode() - Method in class SegmentObjectsFromTensorFlowModel
-
Decodes inference output into segmented objects.
- getDefault() - Static method in class BinaryValues
-
Default values to use, if not otherwise specified
- getDefault() - Static method in class BinaryValuesByte
-
- getDefaultBeanClass() - Method in class AnchorDefaultBeanFactory
-
Returns null as
Optional is not supported by
BeanFactory interface.
- getDefaultColors() - Method in class OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- getDefaultExtension() - Method in interface FileFormat
-
The default extension to write associated with a particular format.
- getDefaultExtension() - Method in enum ImageFileFormat
-
- getDefaultExtension() - Method in enum NonImageFileFormat
-
- getDefaultInstances() - Method in class AnchorDefaultBeanFactory
-
- getDefaultInstances() - Static method in class RegisterBeanFactories
-
- getDefine() - Method in class MarkEvaluator
-
- getDefine() - Method in class DefineOutputter
-
- getDefine() - Method in class Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- getDefine() - Method in class ExportReportFeaturesFromMulti
-
- getDefine() - Method in class FromObjects
-
- getDefine() - Method in class ExportObjectsAsCroppedImages
-
- getDefine() - Method in class SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- getDelaySizeAtEnd() - Method in class MovieFromSlices
-
- getDelegate() - Method in class RasterGeneratorDelegateToRaster
-
- getDelegate() - Method in class UnsignedByteBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class UnsignedIntBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class UnsignedShortBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class InputFromManagerDelegate
-
- getDelegate() - Method in class BoundMinMax
-
- getDelegate() - Method in class CalculateInputFromDelegate
-
- getDelimiter() - Method in class SubsetRangeIfRequested
-
Character used to split the name into groups.
- getDelimiter() - Method in class LastDirectoryAsPrefix
-
- getDelta() - Method in class Mser
-
- getDeltat() - Method in class AnisotropicDiffusion
-
- getDepth() - Method in class TraversalResult
-
The depth of directories processed, where 1 = root directory traversed, 2 = root directory +
one further level etc.
- getDepth() - Method in class ImposeResolution
-
Physical pixel size of a voxel in z-dimension.
- getDerivePath() - Method in class AnnotationMarksComparer
-
- getDerivePath() - Method in class MarksComparer
-
- getDerivePath() - Method in class MaskComparer
-
- getDerivePath() - Method in class ObjectComparer
-
- getDerivePath() - Method in class CollapseFileName
-
- getDerivePath() - Method in class RemoveTrailingDirectory
-
- getDescription() - Method in class OutputtedFile
-
- getDescription() - Method in class ManifestDirectoryDescription
-
- getDescription() - Method in class KernelDescision
-
- getDescription() - Method in class KernelWithIdentifier
-
- getDestination() - Method in class IdentifiablePair
-
- getDestination() - Method in class PairPxlMarkMemo
-
- getDestination() - Method in class DualVoxelizedMarks
-
- getDestination() - Method in class ToPixelized
-
- getDestinationDirectory() - Method in class CopyContext
-
Destination directory for copying.
- getDictionaries() - Method in class DictionaryInitialization
-
- getDictionary() - Method in class ParametersAsFeatures
-
- getDictionary() - Method in class FeatureInitialization
-
- getDictionary() - Method in class EnergyStack
-
- getDictionary() - Method in class FeaturesInitialization
-
- getDictionary() - Method in class FeatureEvaluator
-
Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
- getDictionary() - Method in class EnergySchemeCreatorByElement
-
- getDictionary() - Method in class ScaleByParams
-
- getDictionary() - Method in class AssignFromDictionary
-
The dictionary from which an assignment will occur.
- getDictionary() - Method in class ScoreVoxels
-
- getDictionary() - Method in class IfParamEqual
-
- getDictionary() - Method in class DictionaryCondition
-
The dictionary to provide a value to check.
- getDictionary() - Method in class FeatureListProviderLDAClassifier
-
- getDictionary() - Method in class FeatureValueCheckMark
-
- getDictionary() - Method in class DefineOutputterWithEnergy
-
- getDictionary() - Method in class GaussianSampler
-
The dictionary that parameterizes the Gaussian-distribution that is sampled from.
- getDictionary() - Method in class Develop
-
If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
- getDictionary() - Method in class SegmentMarksFromImage
-
If non-empty, the identifier of a key-value-params collection that is passed to the
segmentation procedure.
- getDimensions() - Method in class ReportFeatureForMarks
-
- getDimensions() - Method in class FromDimensionsBase
-
- getDimensions() - Method in class FromDimensionsBase
-
- getDimensions() - Method in class RepeatSlice
-
Dimensions to create new mask
- getDimensions() - Method in class MergeBase
-
- getDimensions() - Method in class WithDimensionsBase
-
- getDimensions() - Method in class WithOptionalDimensionsBase
-
- getDimensions() - Method in class ToDimensions
-
The dimensions the source image/entity is desired to be scaled to.
- getDimensions() - Method in class FromMarks
-
- getDimensions() - Method in class RequireFeatureRelationThreshold
-
- getDimensions() - Method in class PointsFitterToMark
-
- getDimensionsOptional() - Method in class FeatureInputMark
-
- getDimensionsRequired() - Method in class FeatureInputMark
-
- getDimensionsSourceFallback() - Method in class ToDimensions
-
- getDirection() - Method in class ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- getDirection() - Method in class FeatureMarkDirection
-
- getDirectionVector() - Method in class LineSegment
-
- getDirectionVector() - Method in class FromUnitValueDistance
-
- getDirectory() - Method in class PathDifference
-
The directory component of the difference, if it exists.
- getDirectory() - Method in class InputArguments
-
A directory indicating where inputs can be located
- getDirectory() - Method in class FilesProviderWithDirectoryString
-
A directory in which to look for files.
- getDirectory() - Method in class FileWithDirectoryInput
-
A directory that must be a containing directory (at some hierarchical level) of file
associated with this input.
- getDirectory() - Method in class GlobExtractor.GlobWithDirectory
-
The directory part of the string, or null if it doesn't exist
- getDirectory() - Method in class DualPathPredicates
-
Only accepts any containing directories where the predicate returns true
- getDirectory() - Method in class OutputterTarget
-
- getDirectory() - Method in class DirectoryWithPrefix
-
- getDirectory() - Method in class HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- getDirectoryAsPath(InputContextParams) - Method in class FilesProviderWithDirectory
-
- getDirectoryAsPath(InputContextParams) - Method in class FilesProviderWithDirectoryString
-
- getDirectoryAsPath(InputContextParams) - Method in class FilesProviderWithDirectoryUnary
-
- getDirectoryAsPath(InputContextParams) - Method in class SingleFile
-
- getDirectoryAsPathEnsureAbsolute(InputContextParams) - Method in class FilesProviderWithDirectory
-
Like getDirectory as Path but converts any relative path to absolute one
- getDirectoryDataset() - Method in class QuickMultiDatasetExperiment
-
- getDirectoryDistance() - Method in class QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- getDirectoryOutput() - Method in class QuickExperiment
-
- getDistance() - Method in class DistanceIndex
-
- getDistance() - Method in class DistanceIndexTwice
-
- getDistance() - Method in class LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching
neighbors, distance==2 implies those touching the directly touching etc.)
- getDistanceMapProvider() - Method in class MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- getDistanceMax() - Method in class CalculateLevel
-
- getDistanceTransformMultiplyBy() - Method in class AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short
- getDistanceTransformSmoothSigmaMeters() - Method in class AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters
below
- getDistanceX() - Method in class ReflectInAxesWithinDistance
-
- getDistanceY() - Method in class ReflectInAxesWithinDistance
-
- getDistanceZ() - Method in class ReflectInAxesWithinDistance
-
- getDistanceZEndIfEmpty() - Method in class XYOrientationExtendToZ
-
- getDivideByZeroValue() - Method in class Divide
-
- getDivisor() - Method in class PermutePropertySequenceDouble
-
Divide by
- getDivisor() - Method in class IdentifierModulo
-
What the identifier is divided by to find the modulo.
- getDoubleOrNull(int) - Method in class ResultsVector
-
- getDrawObject() - Method in class SimpleOverlayWriter
-
- getDrawObject() - Method in class DrawOverlay
-
- getDscr() - Method in exception AnchorCombinableException
-
- getDscr() - Method in class ResolvedBound
-
- getDualStack() - Method in class OptimizationContext
-
- getEigenvalue() - Method in class EigenvalueAndVector
-
- getEigenvector() - Method in class EigenvalueAndVector
-
- getElemAllAsFeatureList() - Method in class EnergyScheme
-
- getElemAllCreator() - Method in class EnergySchemeCreatorByElement
-
- getElemByCliqueSize(int) - Method in class EnergyScheme
-
- getElement() - Method in class LabelledWithConfidence
-
- getElement() - Method in class WithConfidence
-
- getElemIndAsFeatureList() - Method in class EnergyScheme
-
- getElemIndCreator() - Method in class EnergySchemeCreatorByElement
-
- getElemPairAsFeatureList() - Method in class EnergyScheme
-
- getElemPairCreator() - Method in class EnergySchemeCreatorByElement
-
- getEllipseSum(double, double, DoubleMatrix2D) - Static method in class Ellipse
-
- getEllipsoidCalculator() - Method in class Ellipsoid
-
- getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class Ellipsoid
-
- getElseName() - Method in class FileNamerContext
-
A fallback name, if a failure occurs when naming.
- getEmptyValue() - Method in class CenterOfGravity
-
- getEmptyValue() - Method in class Intersection
-
- getEmptyValue() - Method in class ArbitraryInsidePoint
-
- getEmptyValue() - Method in class IntensityMeanMaxSlice
-
- getEmptyValue() - Method in class IntensityMeanShellBase
-
- getEmptyValue() - Method in class DerivedObject
-
- getEnd() - Method in class SequenceInteger
-
An index beyond which we cannot iterate (inclusive)
- getEndIndex() - Method in class IndexRange
-
The index if the last element to use in the subsetting range, inclusive.
- getEndPoint() - Method in class LineSegment
-
- getEnergy() - Method in class Aggregator
-
- getEnergyChannelIndex() - Method in class Identity
-
- getEnergyChannelIndex() - Method in class RejectIfIntensityLessThan
-
- getEnergyChannelIndex() - Method in class SingleChannel
-
- getEnergyChannelIndex() - Method in class QuantileAcrossConnectedComponents
-
- getEnergyChannelIndexCheck() - Method in class IdentityImposeValueRelationToHistogram
-
- getEnergyChannelIndexFail() - Method in class IdentityImposeValueRelationToHistogram
-
- getEnergyIndex() - Method in class NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- getEnergyIndex() - Method in class OutsideRange
-
- getEnergyIndex() - Method in class Intensity
-
The channel that that forms the histogram
- getEnergyIndex() - Method in class AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's
dimensions
- getEnergyIndex() - Method in class OverlapMaskBase
-
- getEnergyIndexGradient() - Method in class TextureScore
-
- getEnergyIndexMask() - Method in class IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for
ON and OFF
- getEnergyIndexMask() - Method in class Intensity
-
Optionally, index of another channel that masks the histogram.
- getEnergyIndexX() - Method in class IntensityGradientBase
-
- getEnergyIndexY() - Method in class IntensityGradientBase
-
- getEnergyIndexZ() - Method in class IntensityGradientBase
-
- getEnergyScheme() - Method in class MarksWithEnergyBreakdown
-
- getEnergyScheme() - Method in class MarksWithTotalEnergy
-
Associated Energy Scheme, which should include the EnergySavedPairs
- getEnergyScheme() - Method in class VoxelizedMarksWithEnergy
-
- getEnergyScheme() - Method in class EnergySchemeWithSharedFeatures
-
- getEnergyScheme() - Method in class KernelCalculationContext
-
- getEnergyScheme() - Method in class OptimizationContext
-
- getEnergySchemeCreator() - Method in class MarkEvaluator
-
- getEnergySchemeCreator() - Method in class SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- getEnergyStack() - Method in class FeatureInitialization
-
- getEnergyStack() - Method in class ProposerContext
-
- getEnergyStack() - Method in class DualStack
-
The energy-stack
- getEnergyStack() - Method in class FeatureCalculatorFromProvider
-
- getEnergyStack() - Method in class InitializationWithEnergyStack
-
- getEnergyStackOptional() - Method in class FeatureInputEnergy
-
Returns the energy-stack which may or not be present
- getEnergyStackRequired() - Method in class FeatureInputEnergy
-
Returns the energy-stack or throws an exception if it's not set as it's required.
- getEnergyTotal() - Method in class EnergyPair
-
- getEnergyTotal() - Method in class MarksWithEnergyBreakdown
-
- getEnergyTotal() - Method in class MarksWithTotalEnergy
-
The pre-annealed total energy
- getEnergyTotal() - Method in class VoxelizedMarksWithEnergy
-
- getEnergyTotal() - Method in class EnergySavedAll
-
- getEnergyTotal() - Method in class EnergySavedInd
-
- getEnergyTotal() - Method in class EnergySavedPairs
-
Pairwise energy total
- getEquals() - Method in class FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- getErrorMessage() - Method in class ErrorNodeImpl
-
- getErrorNode() - Method in class ProposerContext
-
- getErrorReporter() - Method in interface InputOutputContext
-
The associated error reporter.
- getErrorReporter() - Method in class Outputter
-
- getErrorReporter() - Method in class GraphLogger
-
- getErrorTree() - Method in class ProposerFailureDescription
-
- getExactDepth() - Method in class DirectoryDepth
-
- getException() - Method in exception CheckedStream.ConvertedToRuntimeException
-
- getException(String) - Method in interface NamedProvider
-
Retrieves the item if it exists, or throws an exception if it doesn't exist.
- getException(String) - Method in class LazyEvaluationStore
-
- getException(int) - Method in class ResultsVector
-
- getException(String) - Method in class SharedFeatureSet
-
- getException(String) - Method in class NamedEntries
-
- getExecutionTime() - Method in class KernelDescision
-
- getExecutionTime() - Method in class Reporting
-
- getExperiment() - Method in class ExperimentResultsExperimentStructure
-
- getExperiment() - Method in class ExperimentStructure
-
- getExperimentalManifest() - Method in class ParametersExperiment
-
- getExperimentArguments() - Method in class InputOutputContextStateful
-
- getExperimentArguments() - Method in class ParametersExperiment
-
- getExperimentDescription() - Method in class OptimizationContext
-
- getExperimentIdentifier() - Method in class OutputExperiment
-
A name for the experiment.
- getExperimentIdentifier() - Method in class ParametersExperiment
-
- getExperimentManifest() - Method in class CoupledManifests
-
- getExperimentType() - Method in class FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same
directory
- getExperimentType() - Method in class QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- getExperimentType() - Method in class RootedExperiment
-
A directory identifying the type of experiment.
- getExpression() - Method in class RegExSimple
-
A Java-style regular expression containing groups.
- getExpression() - Method in class MatchRegularExpression
-
- getExpression() - Method in class RegularExpression
-
- getExtension() - Method in class FilenameSplitExtension
-
The extension of the filename.
- getExtension() - Method in class OneOrThreeChannelsWriter
-
- getExtension() - Method in class AppendStack
-
- getExtension() - Method in class AppendStackDirect
-
- getExtensions() - Method in class MatchExtensions
-
A set of file-extensions (without the period), one of which must match the end of a path.
- getExtensions() - Method in class BranchExtension
-
Any extensions to match (case insensitive) not including any leading period.
- getExtent() - Method in class KernelPointCursor
-
- getExtractScoreSize() - Method in class DirectAssignMode
-
- getExtractScoreSize() - Method in class UniformProposal
-
- getExtractScoreSizeReport() - Method in class TransformationAssignMode
-
- getExtractScoreSizeState() - Method in class TransformationAssignMode
-
- getExtractWeight() - Method in class KernelInitialMarksFromPartition
-
- getExtraLength() - Method in class Midpoint
-
- getFactor() - Method in class ScoreObjects
-
- getFactor() - Method in class Scale
-
- getFactorHigh() - Method in class Identity
-
- getFactorLow() - Method in class Identity
-
- getFactorStandardDeviation() - Method in class GaussianSampler
-
Multiples the standard deviation of the distribution found in keyStandardDeviation.
- getFallback() - Method in class SpecificPathList
-
If no paths can be found either from listPaths or the input-context, then the fallback is
called if exists, otherwise an error is thrown
- getFallback() - Method in class ToSuggested
-
- getFallback() - Method in class RGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- getFallbackName() - Method in class ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name
- getFeature() - Method in class ListSequence
-
The list feature that is duplicated, and populated.
- getFeature() - Method in class FeatureProviderDefine
-
- getFeature() - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session.
- getFeature() - Method in class OutputFeatureTable
-
A list of features to calculate in an evaluation context.
- getFeature() - Method in class ScoreObjects
-
Feature that calculates the score for an object.
- getFeature() - Method in class PermuteFeatureBase
-
- getFeature() - Method in class AddCriteriaFeatureRelationThreshold
-
- getFeature() - Method in class FeatureValueCheckMark
-
- getFeature() - Method in class RequireFeatureRelationThreshold
-
- getFeatureCondition() - Method in class IfCondition
-
- getFeatureCondition() - Method in class IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- getFeatureElse() - Method in class IfCondition
-
- getFeatureEvaluator() - Method in class MultipleComparer
-
- getFeatureEvaluator() - Method in class ReportFeatureEvaluator
-
- getFeatureEvaluator() - Method in class FeatureCostAssigner
-
- getFeatureEvaluator() - Method in class DiscardOutliers
-
- getFeatureEvaluator() - Method in class RelationWithMatches
-
- getFeatureEvaluator() - Method in class ThresholdedFeature
-
- getFeatureEvaluator() - Method in class ObjectCollectionProviderWithFeature
-
- getFeatureEvaluator() - Method in class MergeGreedyToIncreaseObjectFeature
-
- getFeatureEvaluator() - Method in class MergeToIncreaseObjectFeature
-
- getFeatureEvaluatorMatch() - Method in class RelationWithMatches
-
- getFeatureEvaluatorMerge() - Method in class MergePairs
-
- getFeatureEvaluatorThreshold() - Method in class MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- getFeatureListRef() - Method in class FeatureProviderReference
-
- getFeatureListSet() - Method in class FeaturesInitialization
-
- getFeatureNameIndex() - Method in class FeatureInputResults
-
- getFeatureNames() - Method in class InputProcessContext
-
- getFeatureNames() - Method in class SharedStateExportFeatures
-
- getFeatureProvider() - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- getFeatures() - Method in class FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a
session
- getFeatures() - Method in class ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation)
- getFeatures() - Method in class SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- getFeaturesAggregate() - Method in class ExportFeatures
-
Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
- getFeaturesImage() - Method in class PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every
object.
- getFeaturesPair() - Method in class PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- getFeatureTables() - Method in class Develop
-
Specifies a feature-table that can also be outputted.
- getFeedbackReceiver() - Method in class FeedbackReceiverRequireArguments
-
- getFeedbackReceiver() - Method in class SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- getFile() - Method in class NamedChannelsInputPart
-
- getFile() - Method in class NamedFile
-
The file.
- getFile() - Method in class SingleFileInputBase
-
- getFile() - Method in class DualPathPredicates
-
Only accepts files where the predicate returns true
- getFileExtension() - Method in class FileType
-
- getFileFilter() - Method in class ExperimentResultsExperimentStructure
-
Files to search for
- getFileId() - Method in class AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- getFileId() - Method in class FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- getFileInput() - Method in class GroupFiles
-
- getFileInput() - Method in class NamedChannels
-
- getFileInput() - Method in class Stacks
-
- getFileInput() - Method in class QuickExperiment
-
A string indicating the input file(s)
- getFilename() - Method in class PathDifference
-
The file-name component of the difference, if it exists.
- getFileName() - Method in class OutputtedFile
-
- getFileName() - Method in class ReportFeatureForManifestFileBase
-
- getFilePath() - Method in class SortedSetSlice
-
- getFilePath() - Method in class FromSerializedMarks
-
- getFilePath() - Method in class FromSerializedObject
-
- getFilePathParser() - Method in class MultiFileReader
-
- getFilePathProviderSVM() - Method in class FeatureListProviderSVMClassifier
-
- getFilePaths() - Method in class FilePathInitialization
-
Named-store of file-paths.
- getFilePaths() - Method in class FeaturesInitialization
-
- getFilePrefix() - Method in class MovieFromSlices
-
- getFiles() - Method in class TraversalResult
-
All files in any directories that have been traversed.
- getFiles() - Method in class ReadFromFile
-
Provides a single file containing a dictionary.
- getFiles() - Method in class FilesProviderUnary
-
- getFiles() - Method in class FilesProviderWithDirectoryUnary
-
- getFiles() - Method in class FromFiles
-
A provider that should return exactly one
File whose path is employed.
- getFiles() - Method in class Rooted
-
- getFiles() - Method in class NamedFiles
-
The files to use as inputs.
- getFiles() - Method in class NamedFilesWithDirectory
-
The files to use as inputs.
- getFiles() - Method in class QuickBase
-
A path to the main channel of each file
- getFilter() - Method in class IfObjectFilter
-
- getFilter() - Method in class ObjectCollectionProviderFilterBase
-
- getFilter() - Method in class Filter
-
- getFilter() - Method in class ImageLabellerStringMap
-
- getFilterExtensions() - Method in class InputArguments
-
If defined, a set of extension filters that can be applied on inputDirectory
- getFilterFilesCsv() - Method in class QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- getFilterGlob() - Method in class InputArguments
-
If defined, a glob that is applied on inputDirectory
- getFilterInitialization(Path) - Method in class SharedStateFilteredImageOutput
-
- getFindOutlinePixelAngle() - Method in class TraversePointsOnContour
-
- getFirst() - Method in class CostMatrix
-
- getFirst() - Method in class FeatureInputPairObjects
-
- getFirst() - Method in class OutputEnableRulesSpecify
-
Output-names in the first-level.
- getFirst() - Method in class Compose
-
First transformation from S to U
- getFirst() - Method in class PrecalculationOverlay
-
- getFirstArgument() - Method in class HelpConfig
-
What the application argument is described as in the help message
e.g. experimentFile.xml
- getFirstBinaryValues() - Method in class ObjectCollection
-
- getFirstBinaryValuesByte() - Method in class ObjectCollection
-
- getFirstDimensions() - Method in class StackNotUniformSized
-
- getFirstExtent() - Method in class VoxelsWrapperList
-
- getFirstPoint() - Method in class Contour
-
- getFloat() - Static method in class VoxelsFactory
-
- getFontColor() - Method in class TextStyle
-
Font-color of drawn text
- getFontName() - Method in class TextStyle
-
Font-name of drawn text
- getFontSize() - Method in class TextStyle
-
Font-size of drawn text
- getForAllSlices(int) - Method in class IndexByRegion
-
- getForceReader() - Method in class BioformatsReader
-
If non-empty forces usage of a particular bioformats plugin
- GetForSeries<T,S> - Interface in org.anchoranalysis.plot
-
- getForSlice(int, int) - Method in class IndexByRegion
-
- getFoundDirectory() - Method in class FinderSingleDirectory
-
- getFoundFile() - Method in class FinderSingleFile
-
- getFoundOrLog(String, Logger) - Method in interface Findable
-
Returns the found object (or empty() if it's not found.....
- getFoundOrLog(String, Logger) - Method in class Found
-
- getFoundOrLog(String, Logger) - Method in class NotFound
-
- getFriendlyName() - Method in class Feature
-
- getFriendlyName() - Method in interface InitializableFeature
-
A friendly name that can be displayed to user describing the Feature.
- getFrom() - Method in class TypedEdge
-
The vertex the edge joins from.
- getFunction() - Method in class ManifestDescription
-
Identifies the function the entity plays.
- getGaussianSigmaMeters() - Method in class AddEdgeFilters
-
- getGenerator() - Method in class BoundOutputter
-
The generator to be (repeatedly) used to write elements in the sequence.
- getGeneratorList() - Method in class CombineRasterGenerator
-
- getGlob() - Method in class MatchGlob
-
The string describing a glob e.g.
- getGlob() - Method in class GlobExtractor.GlobWithDirectory
-
- getGradient() - Method in class ScoreVoxels
-
- getGraphColorScheme() - Method in class PlotIndexBase
-
- getGrayscaleReconstruction() - Method in class MinimaImpositionGrayscaleReconstruction
-
- getGreen() - Method in class RGBColorBean
-
- getGreen() - Method in class RGBColor
-
- getGreen() - Method in class ThreeChannels
-
- getGroup() - Method in class RowLabels
-
an identifier for a higher-level group which the row belongs to (foreign key)
- getGroup() - Method in class AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- getGroup() - Method in class ExportFeatures
-
If non-null this file-path is used to determine the group of the file If null, no group is
included.
- getGroup() - Method in class GroupedStackBase
-
If defined, translates a file-path into a group.
- getGroup() - Method in class CSVRow
-
- getGroup() - Method in class AppendHistogram
-
- getGroupGeneratorName() - Method in class InputProcessContext
-
- getGroupHeaders() - Method in class LabelHeaders
-
Headers describing the non-feature columns outputted in the CSV related to identifying the
group of a row
- getGroupMap() - Method in class GroupedSharedState
-
- getGroupNum() - Method in class RootFilePathRegEx
-
- getHeaders() - Method in class FeatureCSVMetadata
-
Headers for the CSV file
- getHeaders() - Method in class CSVReader.OpenedCSVFile
-
- getHeight() - Method in class SizeXY
-
Size in Y dimension.
- getHeight() - Method in class ImposeResolution
-
Physical pixel size of a voxel in y-dimension.
- getHistogram() - Method in class HistogramProviderUnary
-
- getHistogram() - Method in class FeatureInputHistogram
-
- getHistogram() - Method in class ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple
images).
- getHistogram() - Method in class SegmentChannel
-
An optional histogram of voxel intensity values which can be used by segment
- getHistogram() - Method in class PlotHistogram
-
The histogram to plot.
- getHistogram() - Method in class LevelResult
-
- getHistogram() - Method in class FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the
inputted CSV.
- getHistogramChannelIndex() - Method in class CalculateLevelBase
-
- getHistogramIndex() - Method in class IdentityImposeValueRelationToHistogram
-
- getHistogramsExtra() - Method in class ScoreVoxels
-
- getHorizontalAlign() - Method in class Overlay
-
- getId() - Method in class DictionaryProviderReference
-
- getId() - Method in class Reference
-
- getId() - Method in class FeatureProviderReference
-
- getId() - Method in class StatisticForFeature
-
- getId() - Method in class BinarySegmentationReference
-
- getId() - Method in class FilePathProviderReference
-
- getId() - Method in class KernelDescision
-
- getId() - Method in class Reference
-
- getId() - Method in class FromChannel
-
- getId() - Method in class Reference
-
- getId() - Method in class Reference
-
- getId() - Method in class Reference
-
- getId() - Method in class ReferenceOrElse
-
- getId() - Method in class Reference
-
- getId() - Method in class FeatureIntersectingObjects
-
ID for the particular object-collection
- getId() - Method in class ExportFeatures
-
Translates an input file name to a unique ID
- getId() - Method in class MarkBoundsReference
-
- getId() - Method in class MarkProposerReference
-
- getId() - Method in class MarkMergeProposerReference
-
- getId() - Method in class MarkSplitProposerReference
-
- getId() - Method in class Reference
-
- getId() - Method in class ReferenceOrEmpty
-
- getId() - Method in class CreateEllipse
-
- getId() - Method in class CSVRow
-
- getId() - Method in class Reference
-
- getIdentifier(T, int) - Method in interface IdentifierGetter
-
- getIdentifier(T, int) - Method in class IdentifierModulo
-
- getIdentifier(T, int) - Method in class IdentifyByIteration
-
- getIdentifier(ObjectWithProperties, int) - Method in class IdentifierByProperty
-
- getIdentifier() - Method in class NamedFile
-
Unique identifier associated with the file.
- getIdentifier(Mark, int) - Method in class IdentifierFromMark
-
- getIdentifier() - Method in class Mark
-
- getIdentifier() - Method in class OverlayMark
-
- getIdentifier() - Method in class KernelWithIdentifier
-
- getIdentifier() - Method in interface Identifiable
-
- getIdentifier(Overlay, int) - Method in class IdentifierFromOverlay
-
- getIdentifier(ObjectWithProperties, int) - Method in class IdentifyDelegateToOverlays
-
- getIdentifier() - Method in class OverlayObjectMask
-
- getIdentifierSubrange() - Method in class InputArguments
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getIdentifierSubrange() - Method in class InputContextParams
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getIdentifierSuffix() - Method in class QuickMultiDatasetExperiment
-
- getIdentifierSuffix() - Method in class QuickMultiDatasetStructuredExperiment
-
- getIdGenerator() - Method in class ExportObjectsFromCSV
-
- getIdGetter() - Method in class IdentifierModulo
-
- getIdGetter() - Method in class ObjectDrawAttributes
-
Gets a unique ID associated with the object
- getIfPresent(K) - Method in class LRUCache
-
Gets an value if present, but doesn't create any new entry if it's absent.
- getIgnoreContains() - Method in class AnnotationBackground
-
If non-empty any stackNames (after map) containing a certain string will be ignored
- getImage() - Method in class MergedPairsFeatures
-
- getImage() - Method in class PointsInitialization
-
- getImage() - Method in class InitializationWithEnergyStack
-
- getImageDimensions() - Method in class ImageFileShape
-
- getImageLabeller() - Method in class ImageAssignLabel
-
Maps a label to an image
- getImgChannelMapCreator() - Method in class GroupFiles
-
- getIncrement() - Method in class SequenceInteger
-
Size of step to use when incrementing
- getIndex() - Method in class Indexable
-
- getIndex() - Method in interface IndexGetter
-
- getIndex(String) - Method in class NamedFeatureStore
-
- getIndex() - Method in class DistanceIndex
-
- getIndex() - Method in class ChannelEntry
-
- getIndex() - Method in class KernelPointCursor
-
- getIndex() - Method in class OutputtedFile
-
- getIndex(TreeNode) - Method in class ErrorNodeImpl
-
- getIndex() - Method in class KernelDescision
-
- getIndex() - Method in class AtIndex
-
- getIndex() - Method in class SliceAt
-
Index in z-dimension of slice to extract
- getIndex() - Method in class SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue,
1=second-largest eigenvalue etc.)
- getIndex() - Method in class IndexedRegionBase
-
- getIndex() - Method in class OrderedRadius
-
- getIndex() - Method in class AsObject
-
- getIndex() - Method in class HOGFeature
-
Which index to return from the HOG descriptor
- getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class FromCSVSharedState
-
- getIndexEnd() - Method in class ExtractSliceRange
-
Slice index to end extracting from (inclusive).
- getIndexForMemo(VoxelizedMarkMemo) - Method in class EnergyMemoList
-
- getIndexHighest() - Method in class DistanceIndexTwice
-
Highest-level index.
- getIndexLowest() - Method in class DistanceIndexTwice
-
Lowest-level index.
- getIndexNonZero() - Method in class SelectSlicesWithIndexBase
-
- getIndexStart() - Method in class ExtractSliceRange
-
Slice index to start extracting from (inclusive).
- getIndividual() - Method in class MarksWithEnergyBreakdown
-
- getInitContext() - Method in class FeedbackBeginParameters
-
- getInitialization() - Method in class InitializableBean
-
- getInitialization() - Method in class ImageLabellerStringMapInitialization
-
- getInitialKernel() - Method in class KernelProposer
-
- getInitialPoint() - Method in class ContiguousVoxelPath
-
- getInitParamType() - Method in class PropertyInitializer
-
- getInnerCoreDistance() - Method in class Ellipsoid
-
- getInput() - Method in class AnnotationInputManager
-
- getInput() - Method in class InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- getInput() - Method in class InputBound
-
- getInput() - Method in class ParametersUnbound
-
- getInput() - Method in class InputManagerUnary
-
- getInput() - Method in class ExperimentExecutor
-
- getInput() - Method in class MultiInputManager
-
- getInput() - Method in class AnnotationComparisonInputManager
-
- getInput() - Method in class AnnotationComparisonInput
-
- getInput() - Method in class NamedChannelsAppend
-
- getInput() - Method in class Exclude
-
- getInput() - Method in class ConvertNamedChannelsToStack
-
- getInput() - Method in class FromCSVInputManager
-
- getInputContext() - Method in class InputManagerParams
-
- getInputDebug() - Method in class BranchIfDebug
-
- getInputDirectory() - Method in class FileNamerContext
-
A directory associated with the inputs, which if defined, is guaranteed to be a parent of
them all.
- getInputDirectory() - Method in class InputContextParams
-
If defined, a directory which can be used by beans to find input
- getInputFilterExtensions() - Method in class InputContextParams
-
A list of extensions that can be used filter inputs
- getInputFilterGlob() - Method in class InputContextParams
-
A glob that can be used by beans to filter input
- getInputIfPresent(T) - Method in class CacheTransferSource
-
- getInputName() - Method in class MultiInputManager
-
- getInputName() - Method in class QuickExperiment
-
- getInputName() - Method in class MultiInputManagerQuick
-
- getInputOutput() - Method in class InitializationContext
-
The input-output context.
- getInputOutputContext() - Method in class OptimizationContext
-
- getInputPaths() - Method in class InputContextParams
-
A list of paths referring to specific inputs
- getInputPointShift() - Method in class ConicFitterBase
-
- getInstance() - Static method in class InterpolatorFactory
-
- getInt(int) - Method in class VoxelBuffer
-
Gets an element from the buffer at a particular position, converting, if necessary, to an
int.
- getInt(int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- getInt(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- getIntensity() - Method in class ScoreVoxels
-
- getIntensityHistogram() - Method in class BinarySegmentationParameters
-
- getIntensityProvider() - Method in class GenerateString
-
- getInterpolator() - Method in class ScaleXY
-
- getInterpolator() - Method in class OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- getInterpolator() - Method in class ScaleToSize
-
- getItem() - Method in class NamedBean
-
The item that is to be named (i.e.
- getItem() - Method in class SingleContainer
-
- getItem() - Method in class DefineSingle
-
- getItem() - Method in class PrependName
-
- getItem() - Method in class FeatureUnary
-
- getItem() - Method in class FeatureDeriveFromPair
-
- getItem() - Method in class ReportFeatureWrapError
-
- getItem() - Method in class ThresholdHistogram
-
- getItem() - Method in class DeriveFromPair
-
- getItem() - Method in class FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding "aggregate" feature is created in the output
list
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class DerivedObject
-
- getItem() - Method in class FeatureIntersectingObjectsSingleElement
-
- getItem() - Method in class PairedWithMask
-
- getItem() - Method in class RejectIfIntensityLessThan
-
- getItem() - Method in class FeatureSingleObjectFromShared
-
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class AsObjectMask
-
- getItem() - Method in class QuantileAcrossConnectedComponents
-
- getItem() - Method in class Rooted
-
- getItem() - Method in class CoefficientOfVarianceFromAll
-
- getItem() - Method in class MeanFromAll
-
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class FeaturePairMemoOne
-
- getItem1() - Method in class FeatureDoubleElem
-
- getItem2() - Method in class FeatureDoubleElem
-
- getItemMean() - Method in class StatisticalBase
-
- getItemProportionate() - Method in class FeatureAsIndividualProportionate
-
- getItemStdDev() - Method in class StatisticalBase
-
- getIteration() - Method in class Reporting
-
- getIterations() - Method in class AnisotropicDiffusion
-
- getIterations() - Method in class MorphologicalOperatorBase
-
- getIterations() - Method in class ObjectCollectionProviderMorphological
-
- getIterations() - Method in class Repeat
-
The maximum number of iterations.
- getIterations() - Method in class Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- getIterations() - Method in class IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- getIterations() - Method in class Erode
-
- getIterations() - Method in class NumberRemovedVoxelsAfterClosing
-
- getIterations() - Method in class Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- getIterations() - Method in class MorphologicalOperation
-
iterations for erode, dilate, open, close
- getIterations() - Method in class UniformProposal
-
- getIterations() - Method in class NumberIterationsBase
-
The number of iterations for which the number-of-marks must remain constant.
- getIterationsDilation() - Method in class MorphologicalIterations
-
Number of times to perform morphological dilation
- getIterationsErosion() - Method in class MorphologicalIterations
-
Number of times to perform morphological erosion
- getJobDescription() - Method in class SubmittedJob
-
- getJobManifest() - Method in class CoupledManifests
-
- getJobNumber() - Method in class JobDescription
-
- getJobShortName() - Method in class JobDescription
-
- getJobState() - Method in class SubmittedJob
-
- getKappa() - Method in class AnisotropicDiffusion
-
- getKeep() - Method in class MergeCandidate
-
- getKeepProcessorsFree() - Method in class DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- getKeepProcessorsFree() - Method in class ParallelProcessor
-
How many processors to avoid using for the tasks.
- getKernel() - Method in class KernelWithIdentifier
-
- getKernel() - Method in class WeightedKernel
-
- getKernel() - Method in class OptimizationStep
-
- getKernel() - Method in class Reporting
-
- getKernel() - Method in class KernelProposerOptionSingle
-
- getKernelAccepted() - Method in class Aggregator
-
- getKernelApplication() - Method in class DilationContext
-
How the kernel is applied to the scene.
- getKernelCalcContext() - Method in class TransformationContext
-
- getKernelFactoryList() - Method in class FeedbackBeginParameters
-
- getKernelHalfWidth() - Method in class Median
-
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
- getKernelNegative() - Method in class KernelProposerOptionDual
-
- getKernelNoProposalDescription() - Method in class Reporting
-
- getKernelPositive() - Method in class KernelProposerOptionDual
-
- getKernelProposed() - Method in class Aggregator
-
- getKernelProposer() - Method in class SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- getKernelStateBridge() - Method in class TransformationAssignMode
-
- getKey() - Method in exception GetOperationFailedException
-
- getKey() - Method in class AssignFromDictionary
-
The key of the value in the dictionary that will be assigned.
- getKey() - Method in class IfParamEqual
-
- getKey() - Method in class DictionaryCondition
-
The key in the dictionary whose value is checked.
- getKey() - Method in class ParamFromCollection
-
- getKey() - Method in class FilePathParser
-
- getKey() - Method in class RegularExpression
-
- getKey() - Method in class FromDictionary
-
- getKeyGroupID() - Method in class RegularExpression
-
- getKeyLower() - Method in class ScaleByParams
-
- getKeyMean() - Method in class GaussianSampler
-
The name of the key in the dictionary with the mean of the distribution.
- getKeyPrefix() - Method in class FromDictionary
-
Prefix prepended to key
- getKeyStandardDeviation() - Method in class GaussianSampler
-
The name of the key in the dictionary with the standard-deviation.
- getKeySuffix() - Method in class FromDictionary
-
- getKeyUpper() - Method in class ScaleByParams
-
- getLabel() - Method in class ImageLabelAnnotation
-
The label that applies to the image
- getLabel() - Method in class StackProviderWithLabel
-
- getLabel() - Method in class LabelledWithConfidence
-
The label associated with the element.
- getLabelMap() - Method in class ImageCSVLabellerInitialization
-
- getLabels() - Method in class PlotIndexBase
-
- getLabels() - Method in class WholeImageLabelStrategy
-
- getLastDivider() - Method in class Aggregator
-
- getLastPoint() - Method in class Contour
-
- getLastPoints1() - Method in class MarkMergeProposer
-
- getLastPoints2() - Method in class MarkMergeProposer
-
- getLeafDirectories() - Method in class TraversalResult
-
All the directories in the bottom-most depth that was traversed.These directories were not
traversed
- getLeft() - Method in class ObjectsToCompare
-
Objects on left-side of the comparison
- getLevel() - Method in class Constant
-
- getLevel() - Method in class LevelResult
-
- getLine() - Method in class CSVRow
-
- getList() - Method in class Concatenate
-
- getList(Class<?>) - Method in class Define
-
- getList() - Method in class RegExList
-
- getList() - Method in class StringMap
-
- getList() - Method in class ToMultiple
-
The list of loggers to log to
- getList() - Method in class MessageLoggerList
-
- getList() - Method in class Define
-
- getList() - Method in class DefinedNamed
-
- getList() - Method in class FeatureList
-
- getList() - Method in class FeatureListElem
-
- getList() - Method in class ArrangeRaster
-
- getList() - Method in class Combine
-
- getList() - Method in class TileWithLabels
-
- getList() - Method in class FinderExperimentFileDirectories
-
- getList() - Method in class RegionMap
-
- getList() - Method in class AddCriteriaOr
-
- getList() - Method in class FeedbackReceiverList
-
- getList() - Method in class TerminationConditionListOr
-
- getList() - Method in class Concatenate
-
- getList() - Method in class CalculateLevelListBase
-
- getList() - Method in class ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- getList() - Method in class Concatenate
-
- getList() - Method in class Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor
becomes the input of the sucecssor)
- getList() - Method in class Concatenate
-
- getList() - Method in class SpecificAndRename
-
- getList() - Method in class FromEntries
-
- getList() - Method in class Combine
-
- getList() - Method in class Concatenate
-
- getList() - Method in class SummarizerAggregate
-
- getList() - Method in class AndList
-
- getList() - Method in class VisitSchedulerAnd
-
- getList() - Method in class VisitSchedulerUniformSample
-
- getList() - Method in class MarkProposerFromList
-
- getListAdditionalChannelProviders() - Method in class ScoreObjects
-
- getListAppend() - Method in class NamedChannelsAppend
-
- getListAppend() - Method in class MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- getListComparers() - Method in class MultipleComparer
-
- getListFeatures() - Method in class BinaryClassifierImageLabeller
-
- getListFromManager(MultiInputManager) - Method in class AppendDictionary
-
- getListFromManager(MultiInputManager) - Method in class AppendFilePath
-
- getListFromManager(MultiInputManager) - Method in class AppendHistogram
-
- getListFromManager(MultiInputManager) - Method in class AppendMarks
-
- getListFromManager(MultiInputManager) - Method in class AppendObjects
-
- getListFromManager(MultiInputManager) - Method in class AppendStack
-
- getListFromManager(MultiInputManager) - Method in class AppendStackDirect
-
- getListFromManager(MultiInputManager) - Method in class FilePathBaseAppendToManager
-
- getListImageFeatures() - Method in class EnergySchemeCreatorByElement
-
- getListImageFeatures() - Method in class EnergyScheme
-
- getListPaired(boolean) - Method in interface Assignment
-
- getListPaired(boolean) - Method in class AssignmentMaskIntersection
-
- getListPaired(boolean) - Method in class AssignmentOverlapFromPairs
-
- getListPaths() - Method in class SpecificPathList
-
If specified, this forms the list of paths which is provided as input.
- getListReportFeatures() - Method in class ExportReportFeatures
-
- getListStackProvider() - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getListStackProviderMIP() - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getListUnassigned(boolean) - Method in interface Assignment
-
- getListUnassigned(boolean) - Method in class AssignmentMaskIntersection
-
- getListUnassigned(boolean) - Method in class AssignmentOverlapFromPairs
-
- getListUnassignedLeft() - Method in class AssignmentOverlapFromPairs
-
- getListUnassignedRight() - Method in class AssignmentOverlapFromPairs
-
- getLocal(int) - Method in interface BufferRetriever
-
All local access is indexed relative (e.g.
- getLocal(int) - Method in class LocalSlices
-
- getLocalPath() - Method in class AnchorBean
-
A local path on the filesystem associated with this bean (from serialization) if defined.
- getLog() - Method in class OnlyIf
-
The logger to use if conditions are fulfilled
- getLogExperiment() - Method in class OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- getLogExperimentPath() - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- getLogger() - Method in class InitializableBean
-
The logger
- getLogger() - Method in class CommonContext
-
The logger
- getLogger() - Method in class InitializationContext
-
- getLogger() - Method in class InputBound
-
- getLogger() - Method in class InputOutputContextStateful
-
- getLogger() - Method in class InputManagerParams
-
- getLogger() - Method in class FileNamerContext
-
Logs information messages.
- getLogger() - Method in interface InputOutputContext
-
The associated logger.
- getLogger() - Method in class ReporterAggregate
-
- getLogger() - Method in class FeedbackEndParameters
-
- getLogger() - Method in class OptimizationContext
-
- getLogger() - Method in class TransformationContext
-
- getLogger() - Method in class CalculateFeaturesForObjects
-
- getLogger() - Method in class InputProcessContext
-
- getLoggerExperiment() - Method in class ParametersExperiment
-
- getLoggerTaskCreator() - Method in class ParametersExperiment
-
This is a means to create new log-reporters for each task.
- getLogReporterJob() - Method in class InputBound
-
- getLogTask() - Method in class InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- getLogTaskPath() - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- getMainChannelIndex() - Method in class NamedChannelsQuick
-
Index of the mainChannel
- getMainChannelName() - Method in class NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- getMainObjectName() - Method in class MultiInput
-
- getMainObjectName() - Method in class StackWithMap
-
- getMajorAxisAngle() - Method in class EllipseStandardFormConverter
-
- getMajorAxisSlope() - Method in class EllipseStandardFormConverter
-
- getManifest() - Method in class InputBound
-
- getManifestDescription() - Method in class OutputPattern
-
A manifest-description for the directory, if defined.
- getManifestDescription() - Method in class FileType
-
- getManifestDescriptionFunction() - Method in class MarksGeneratorBase
-
- getManifestDeserializer() - Method in class CoupledManifestsInputManager
-
- getManifestExperimentInputFileSet() - Method in class CoupledManifestsInputManager
-
- getManifestFunction() - Method in class ObjectSerializerPeriodicReporter
-
- getManifestFunction() - Method in class VoxelizedMarksChangeReporter
-
- getManifestInputFileSet() - Method in class CoupledManifestsInputManager
-
- getMap() - Method in class OperationMap
-
- getMap() - Method in class ImageLabellerStringMap
-
- getMap() - Method in class ImageLabellerStringMapInitialization
-
- getMapping() - Method in class AnonymizeSharedState
-
- getMark() - Method in class FeatureInputMark
-
- getMark() - Method in class VoxelizedMarkMemo
-
The associated mark
- getMark() - Method in class OverlayMark
-
- getMark() - Method in class KernelDeath.MarkAnd
-
- getMark() - Method in class ObjectWithEllipse
-
- getMarkBounds() - Method in class MarkBoundsDefine
-
- getMarkBounds() - Method in class SegmentThresholdAboveMinBound
-
- getMarkEvaluator() - Method in class MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- getMarkFactory() - Method in class MarkEvaluator
-
- getMarkFactory() - Method in class KernelCalculationContext
-
- getMarkFactory() - Method in class MarkFactoryContext
-
- getMarkFactory() - Method in class OptimizationContext
-
- getMarkFactory() - Method in class SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- getMarkFactory() - Method in class FitPointsFromObjects
-
- getMarkFromMarksProposer() - Method in class KernelSplit
-
- getMarkProposer() - Method in class MarkProposerStrategy
-
- getMarkProposer() - Method in class FromMarkProposer
-
- getMarkProposer() - Method in class MergeMarkEllipse
-
- getMarkProposer() - Method in class MarkEllipseSimple
-
- getMarkProposer() - Method in class KernelBirthAndKill
-
- getMarkProposer() - Method in class KernelExchange
-
- getMarkProposer() - Method in class KernelBirthPixelized
-
- getMarkProposerAdditionalBirth() - Method in class KernelBirthAndKill
-
- getMarkProvider() - Method in class CreateMarkFromPoints
-
- getMarkProvider() - Method in class ReportFeatureOnMark
-
- getMarkProvider() - Method in class FromSingleMark
-
- getMarkProvider() - Method in class RequireFeatureRelationThreshold
-
- getMarkRmv() - Method in class KernelDeath
-
- getMarks() - Method in class RandomCollectionWithAddCriteria
-
- getMarks() - Method in class FeatureInputMarkCollection
-
- getMarks() - Method in class IndexableMarksWithEnergy
-
- getMarks() - Method in class MarksWithEnergyBreakdown
-
- getMarks() - Method in class MarksWithTotalEnergy
-
The marks
- getMarks() - Method in class VoxelizedMarksWithEnergy
-
- getMarks() - Method in class ReportFeatureOnMarks
-
- getMarks() - Method in class MarksWithDisplayStack
-
- getMarks() - Method in class ColoredMarks
-
- getMarks() - Method in class MarkCollection
-
- getMarks() - Method in class FromMarks
-
- getMarks() - Method in class ScaleXY
-
- getMarks() - Method in class RetrieveSingleMarkOnly
-
- getMarks() - Method in class ColoredMarks
-
- getMarks() - Method in class MarksFromPartition
-
- getMarksAfter() - Method in class Reporting
-
- getMarksAfterOptional() - Method in class Reporting
-
- getMarksColored() - Method in class ColoredMarksWithDisplayStack
-
- getMarksProposer() - Method in class KernelInitialMarksFromPartition
-
- getMarksProposer() - Method in class KernelInitialMarksProposed
-
- getMarksProposer() - Method in class KernelInitialMarksVoxelized
-
- getMarksReject() - Method in class DualMarksAnnotation
-
Marks covering area that should be rejected, can be null
- getMarksWithTotalEnergy() - Method in class MarksWithEnergyBreakdown
-
- getMask() - Method in class MaskProviderUnary
-
- getMask() - Method in class FromMaskBase
-
- getMask() - Method in class UnaryWithMaskBase
-
- getMask() - Method in class ScoreVoxels
-
- getMask() - Method in class FromChannel
-
- getMask() - Method in class SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask
has an ON voxel
- getMask() - Method in class ConnectedComponentsFromMask
-
- getMask() - Method in class AndObjectsWithMasks
-
- getMask() - Method in class FromMask
-
- getMask() - Method in class SegmentChannel
-
- getMask() - Method in class ColoredMask
-
- getMask() - Method in class FromChannelOrMask
-
A mask that is provided to the stack.
- getMask() - Method in class PairedWithMask
-
- getMask() - Method in class MaskAsSingleObject
-
- getMask() - Method in class FillHoles
-
- getMask() - Method in class CheckMarkWithMask
-
- getMask() - Method in class FindPointOnOutlineWalk
-
- getMask() - Method in class XYOrientationExtendToZ
-
- getMaskElse() - Method in class IfPredicateBase
-
Returned instead of mask if the predicate is not satisfied
- getMaskFilled() - Method in class TraverseOutlineOnImage
-
- getMaskFilled() - Method in class XYOrientationExtendToZ
-
- getMaskIndex() - Method in class SurfaceSizeMaskNonZero
-
- getMaskOutline() - Method in class TraverseOutlineOnImage
-
- getMaskValue() - Method in class ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- getMaskValue() - Method in class OverlapMaskBase
-
- getMatch() - Method in class SelectFromShared
-
- getMatch() - Method in class FilterCsvColumn
-
- getMatch() - Method in class MatchedAppendCsv
-
- getMatcher() - Method in class SearchDirectory
-
- getMatcher() - Method in class MatchExtensions
-
- getMatcher() - Method in class RelationWithMatches
-
- getMatcher() - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- getMatcher() - Method in class Match
-
- getMatches() - Method in class MatchedObject
-
The matches associated with the source-object
- getMatrix() - Method in class CostMatrix
-
A two-dimensional array mapping the costs from first to second
- getMatrix() - Method in class RotationMatrix
-
The underlying matrix used internally in the rotation-matrix.
- getMax() - Method in interface Progress
-
- getMax() - Method in class ProgressConsole
-
- getMax() - Method in class ProgressIgnore
-
- getMax() - Method in class ProgressIncrement
-
- getMax() - Method in class ProgressOneOfMany
-
- getMax() - Method in class BoundMinMax
-
- getMax() - Method in class ResolvedBound
-
- getMax() - Method in class PointListBase
-
- getMax() - Method in class ScaleByMinMaxValue
-
- getMax() - Method in class ClampHistogramMax
-
- getMax() - Method in class UnitsWithinRange
-
Maximum-boundary for acceptable range
- getMax() - Method in class OutsideRange
-
- getMax() - Method in class MaxOverlapRatio
-
- getMax() - Method in class InvertedMax
-
- getMax() - Method in class CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- getMax() - Method in class RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- getMaxBin() - Method in class Histogram
-
Maximum bin-value inclusive
- getMaxCost() - Method in class MultipleComparer
-
- getMaxCost() - Method in class FeatureCostAssigner
-
- getMaxDirectoryDepth() - Method in class SearchDirectory
-
If non-negative the max depth of directories.
- getMaxDirectoryDepth() - Method in class PathMatchConstraints
-
Limits on the depth of how many sub-directories are recursed
- getMaxDirectoryDepth() - Method in class ExperimentResultsExperimentStructure
-
- getMaxDistance() - Method in class MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- getMaxDistance() - Method in class CostOverlapWithinMidpointDistance
-
- getMaxDistance() - Method in class FindPointOnOutlineWalk
-
- getMaxDistanceBetweenMinima() - Method in class AddDistanceTransform
-
- getMaxDistanceCOG() - Method in class MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- getMaxDistanceDeltaContour() - Method in class AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- getMaxDistanceDeltaContour() - Method in class MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the
distanceMap for each point.
- getMaxDistanceProposer() - Method in class VisitSchedulerMaxDistanceAlongContour
-
- getMaxDistanceZ() - Method in class XYOrientationExtendToZ
-
- getMaximumIndex() - Method in class BoundedIndexContainerFromList
-
- getMaximumIndex() - Method in interface BoundedRange
-
- getMaximumIndex() - Method in class BoundsFromRange
-
- getMaximumIndex() - Method in class BoundedIndexContainerBridge
-
- getMaximumIndex() - Method in class IntegerSequenceContaner
-
- getMaximumIndex() - Method in class SingleContainer
-
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class RadiiProposerRepeat
-
- getMaxNumberItems() - Method in class Limit
-
- getMaxNumberItems() - Method in class Limit
-
- getMaxNumberProcessors() - Method in class TaskArguments
-
Suggests a maximum number of processors (CPUs) for a task.
- getMaxNumberProcessors() - Method in class DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- getMaxNumberProcessors() - Method in class ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- getMaxNumberProcessors() - Method in class QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- getMaxNumberProcessors() - Method in class QuickMultiDatasetStructuredExperiment
-
- getMaxNumItems() - Method in class LimitWithDirectory
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- getMaxScaleFactor() - Method in class LargestMultipleWithin
-
An upper limit on the scale-factor allowed in each dimension.
- getMaxSize() - Method in class Mser
-
- getMaxSplitGroups() - Method in class CompareAnnotations
-
- getMaxValue() - Method in class ConsistentChannelChecker
-
- getMaxVar() - Method in class Mser
-
- getMaxVolume() - Method in class FillHoles
-
- getMaxX() - Method in class InsideBoxOn
-
Maximum X coordinate inclusive
- getMaxY() - Method in class InsideBoxOn
-
Maximum Y coordinate inclusive
- getMaxZ() - Method in class InsideBoxOn
-
Maximum Z coordinate inclusive
- getMean() - Method in class FirstSecondOrderStatistic
-
Mean
- getMean(int) - Method in class ImageMoments
-
Index is the axis (0 for X, 1 for Y, 2 for Z)
- getMedianRadiusMeters() - Method in class AddEdgeFilters
-
- getMemoForIndex(int) - Method in class VoxelizedMarksWithEnergy
-
- getMemoForIndex(int) - Method in class EnergyMemoList
-
- getMemoForIndex(int) - Method in class MemoList
-
- getMemoForIndex(int) - Method in interface MemoForIndex
-
- getMemoForMark(Mark) - Method in class VoxelizedMarksWithEnergy
-
- getMemoForMark(MarkCollection, Mark) - Method in class EnergyMemoList
-
- getMemoized() - Method in class FinderSerializedObject
-
Provides a memoized (cached) means of access the results of the finder
- getMerge() - Method in class MergeCandidate
-
- getMerged() - Method in class FeatureInputPairObjects
-
Returns a merged version of the two-objects available (or null if not available)
- getMergedOptional() - Method in class FeatureInputPairObjects
-
- getMergedPosTolerance() - Method in class MergeMarkEllipse
-
- getMergeMarkProposer() - Method in class KernelMerge
-
- getMessage() - Method in exception GetOperationFailedException
-
- getMessage() - Method in class ReportFeatureWrapError
-
- getMessageLogger() - Method in class InputOutputContextStateful
-
- getMessageNoInputs() - Method in class InputOutputExperiment
-
A message written to the logger if no inputs exist for the experiment, and it thus ends
early.
- getMessageReporter() - Method in interface InputOutputContext
-
The associated message reporter.
- getMethod() - Method in class AutoLocalThreshold
-
- getMethod() - Method in class ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string
for the default).
- getMethod() - Method in class CopyFiles
-
How the copying occurs from source to destination file.
- getMiddlePoint() - Method in class Contour
-
- getMin() - Method in interface Progress
-
- getMin() - Method in class ProgressConsole
-
- getMin() - Method in class ProgressIgnore
-
- getMin() - Method in class ProgressIncrement
-
- getMin() - Method in class ProgressOneOfMany
-
- getMin() - Method in class BoundMinMax
-
- getMin() - Method in class ResolvedBound
-
- getMin() - Method in class PointListBase
-
- getMin() - Method in class ScaleByMinMaxValue
-
- getMin() - Method in class UnitsWithinRange
-
Minimum-boundary for acceptable range
- getMin() - Method in class OutsideRange
-
- getMin(Function<FileDetails, Optional<Integer>>) - Method in class ParsedFilePathBag
-
- getMin() - Method in class RadiiMinRatio
-
- getMin() - Method in class CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- getMin() - Method in class RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- getMinConfidence() - Method in class ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be included.
- getMinConfidence() - Method in class DecodeMaskRCNN
-
Only proposals outputted from the model with a score greater or equal to this threshold are
considered.
- getMinConfidence() - Method in class DecodeText
-
Proposed bounding boxes below this confidence interval are removed
- getMinDiff() - Method in class MeanIntensityDifference
-
- getMinDifference() - Method in class Difference
-
A minimum difference, below which 0.0 is returned
- getMinDifference() - Method in class DifferenceCalculateLevelStandardDeviation
-
- getMinDiversity() - Method in class Mser
-
- getMinimaImposition() - Method in class ImposeMinima
-
- getMinimumBoundingBoxVolume() - Method in class FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- getMinimumIndex() - Method in class BoundedIndexContainerFromList
-
- getMinimumIndex() - Method in interface BoundedRange
-
- getMinimumIndex() - Method in class BoundsFromRange
-
- getMinimumIndex() - Method in class BoundedIndexContainerBridge
-
- getMinimumIndex() - Method in class IntegerSequenceContaner
-
- getMinimumIndex() - Method in class SingleContainer
-
- getMinimumSize() - Method in class LargestMultipleWithin
-
The minimum size in each dimension.
- getMinIntensity() - Method in class RejectIfIntensityLessThan
-
- getMinIntensity() - Method in class ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- getMinIntensityValue() - Method in class MorphologicalOperatorBase
-
- getMinMaskValue() - Method in class DecodeMaskRCNN
-
Threshold above which pixels are considered in the mask.
- getMinMaxIgnoreBeforeIndex() - Method in class LinePlot
-
- getMinNumberObjects() - Method in class DiscardOutliers
-
- getMinNumberPoints() - Method in class SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- getMinNumberVoxels() - Method in class SplitIntoSquares
-
Only includes squares that have at least this number of voxels.
- getMinNumberVoxels() - Method in class ConnectedComponentsFromBinarySegmentation
-
- getMinNumberVoxels() - Method in class ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- getMinNumPoints() - Method in class CreateMarkFromPoints
-
- getMinNumPoints() - Method in class PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- getMinNumSlices() - Method in class XYOrientationExtendToZ
-
- getMinNumZSlices() - Method in class AtLeastZSlices
-
- getMinorAxisAngle() - Method in class EllipseStandardFormConverter
-
- getMinorAxisSlope() - Method in class EllipseStandardFormConverter
-
- getMinOverlap() - Method in class CostOverlapWithinMidpointDistance
-
- getMinRadius() - Method in class LinearLeastSquaresEllipseFitter
-
- getMinRadius() - Method in class LinearLeastSquaresEllipsoidFitter
-
- getMinRadScaleEnd() - Method in class MarkEllipseSimple
-
- getMinRadScaleStart() - Method in class MarkEllipseSimple
-
- getMinRatio() - Method in class DiscardOutliers
-
- getMinResolution() - Method in class MinimumXYResolution
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- getMinSize() - Method in class Mser
-
- getMinusOne() - Method in class SlidingBuffer
-
The voxel-buffer for the slice with the currently selected slice's index -1 or null
if it's the first slice.
- getMinVal() - Method in class FeatureValueCheckMark
-
- getMinVolume() - Method in class ConnectedComponentsFromMask
-
- getMinVolume() - Method in class VolumeMin
-
- getMinVolumeConnectedComponent() - Method in class AddDistanceTransform
-
- getMinX() - Method in class InsideBoxOn
-
Minimum X coordinate inclusive
- getMinY() - Method in class InsideBoxOn
-
Minimum Y coordinate inclusive
- getMinZ() - Method in class InsideBoxOn
-
Minimum Z coordinate inclusive
- getModelBinaryPath() - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb extension, relative to the models/ directory in the Anchor distribution.
- getModelDirectory() - Method in class CommonContext
-
Directory where machine-learning models can be found
- getModelDirectory() - Method in class InputArguments
-
- getModelDirectory() - Method in class InputOutputContextStateful
-
- getModelDirectory() - Method in class ImageInitialization
-
- getModelDirectory() - Method in interface InputOutputContext
-
An input-directory in which models are stored.
- getModelDirectory() - Method in class InputProcessContext
-
- getModelPool() - Method in class SharedStateSegmentInstance
-
- getModelTextGraphPath() - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb.txt extension, relative to the models/ directory in the Anchor distribution.
- getMultipleComparer() - Method in class MarkProposerStrategy
-
- getMultiplyBy() - Method in class DistanceTransform3D
-
- getName() - Method in class FromXmlList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- getName() - Method in class NamedBean
-
The name associated with item
- getName(S) - Method in interface ApplyPermutations.NameGetter
-
- getName() - Method in class RootPath
-
- getName() - Method in interface NameValue
-
The associated name
- getName() - Method in class SimpleNameValue
-
- getName() - Method in class ExperimentIdentifierConstant
-
- getName() - Method in class ChannelEntry
-
- getName() - Method in class OptionalNameValue
-
An optional-name.
- getName() - Method in class IncreasingIntegers
-
- getName() - Method in class IncrementingIntegers
-
- getName() - Method in class SequenceType
-
- getName() - Method in class StringsWithoutOrder
-
- getName() - Method in class NamedPath
-
A unique name associated with the path
- getName() - Method in class Circle
-
- getName() - Method in class Ellipse
-
- getName() - Method in class Ellipsoid
-
- getName() - Method in class Sphere
-
- getName() - Method in class Mark
-
- getName() - Method in class LineSegment
-
- getName() - Method in class PointList
-
- getName() - Method in class Polygon
-
- getName() - Method in class PolygonCurve
-
- getName() - Method in class RotatableBoundingBox
-
- getName() - Method in class Kernel
-
- getName() - Method in class WeightedKernel
-
- getName() - Method in class NamedChannel
-
- getName() - Method in class AdjacentFile
-
A name to describe the adjacent file
- getName() - Method in class FilePathAppendBase
-
The name of the appended entity
- getNameLeft() - Method in class AnnotationComparisonInputManager
-
- getNamer() - Method in class GroupFiles
-
- getNamer() - Method in class RemoveExtension
-
- getNamer() - Method in class SubsetRangeIfRequested
-
The namer that is called to provide names that are subsetted.
- getNamer() - Method in class NamedFilesBase
-
- getNamer() - Method in class QuickBase
-
Assigns each input a unique compact name.
- getNameRight() - Method in class AnnotationComparisonInputManager
-
- getNames() - Method in class NamedFeatureCalculatorMulti
-
- getNames() - Method in class AnnotationComparisonInput
-
- getNameSubrange() - Method in class FileNamerContext
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getNameValueSet() - Method in class OverlayProperties
-
- getNaming() - Method in class CopyFiles
-
How an output name (and path) is selected for an input file.
- getNamingSharedState() - Method in class RecordingCounter
-
- getNavigateHigherDirs() - Method in class MultiFileReader
-
Search x number directories higher than file
- getNoProposalReason() - Method in class KernelDescision
-
- getNumberBins() - Method in class HOGParameters
-
The number of bins in each histogram for a cell
- getNumberChannels() - Method in class EnergyStack
-
- getNumberChannels() - Method in class EnergyStackWithoutParams
-
- getNumberChannels() - Method in class DisplayStack
-
- getNumberChannels() - Method in class Stack
-
- getNumberChannels() - Method in class StackNotUniformSized
-
- getNumberChannels() - Method in class ScaleableBackground
-
Number of channels in the stack
- getNumberChannels() - Method in class ForceNumberChannels
-
- getNumberChannels() - Method in class ImageFileShape
-
- getNumberColors() - Method in class TiffTimeSeries
-
- getNumberColumns() - Method in class Tile
-
The number of columns to use in the table produced when tiling.
- getNumberConverter() - Method in class AnonymizeSharedState
-
- getNumberDecimalPlaces() - Method in class FeatureCostAssigner
-
- getNumberDigits() - Method in class IncrementingNumber
-
Number of digits in the number, with leading zeros as necessary.
- getNumberDilations() - Method in class LevelPerObjectIndependently
-
- getNumberDimensions() - Method in class RotationMatrix
-
- getNumberElements() - Method in class IncreasingIntegers
-
- getNumberElements() - Method in class IncrementingIntegers
-
- getNumberElements() - Method in class SequenceType
-
- getNumberElements() - Method in class StringsWithoutOrder
-
- getNumberFrames() - Method in class ForceNumberFrames
-
- getNumberFrames() - Method in class ImageFileShape
-
- getNumberGPUProcessors() - Method in class ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- getNumberKernels() - Method in class KernelProposer
-
- getNumberLevelsGrouping() - Method in class CompareAnnotations
-
- getNumberLoopPoints() - Method in class SplitContourAtSaddlePoints
-
- getNumberPoints() - Method in class LinePlot
-
- getNumberRows() - Method in class Tile
-
The number of rows to use in the table produced when tiling.
- getNumberSeries() - Method in class PlotIndexBase
-
- getNumberSlices() - Method in class ImageFileShape
-
- getNumberSubdirectories() - Method in class LastDirectories
-
How many directories to include in the name.
- getNumCols() - Method in class TileWithLabels
-
- getNumColsUsed() - Method in class TableItemArrangement
-
- getNumMarks() - Method in class FromMarkProposer
-
- getNumRowsUsed() - Method in class TableItemArrangement
-
- getObject() - Method in class Found
-
The found object
- getObject() - Method in class FeatureInputSingleObject
-
- getObject() - Method in class OverlayObjectMask
-
- getObject() - Method in class LevelResult
-
- getObject() - Method in class ObjectVertex
-
- getObject() - Method in class ObjectWithEllipse
-
- getObject1() - Method in class FeatureInputPairMemo
-
- getObject2() - Method in class FeatureInputPairMemo
-
- getObjectMatcher() - Method in class Bridge
-
Used to match each intermediary-object to a final-object
- getObjects() - Method in class ObjectCollectionProviderUnary
-
- getObjects() - Method in class FeatureInputObjectCollection
-
- getObjects() - Method in class OutputFeatureTable
-
The objects for which features are calculated.
- getObjects() - Method in class ReportFeatureOnObjectsBase
-
- getObjects() - Method in class DistanceTransformForEachObject3D
-
- getObjects() - Method in class LevelPerObjectBase
-
The objects for whom a level is calculated
- getObjects() - Method in class UnaryWithObjectsBase
-
- getObjects() - Method in class GenerateToMatchObjects
-
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class IntersectsWith
-
- getObjects() - Method in class Always
-
- getObjects() - Method in class Intersection
-
- getObjects() - Method in class Permute
-
- getObjects() - Method in class ColoredObjects
-
Objects to draw on a background
- getObjects() - Method in class ObjectAggregationBase
-
- getObjects() - Method in class ColoredObjectCollection
-
The objects in the collection.
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class ObjectAsPoints
-
- getObjects() - Method in class IncludeRandomObjects
-
- getObjects() - Method in class PointsFromObjects
-
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class ExportObjectsBase
-
- getObjects() - Method in class PointsFitterToMark
-
- getObjects1() - Method in class MergeTwoCollectionsItemwise
-
First collection with items to be merged
- getObjects2() - Method in class MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- getObjectsBlue() - Method in class ThreeColoredObjects
-
- getObjectsContainer() - Method in class WithContainerBase
-
- getObjectsElse() - Method in class ReferenceOrElse
-
- getObjectsGreater() - Method in class GreaterIntersectionWith
-
- getObjectsGreen() - Method in class ThreeColoredObjects
-
- getObjectsGrouped() - Method in class FilterByGroup
-
- getObjectsLesser() - Method in class GreaterIntersectionWith
-
- getObjectsRed() - Method in class ThreeColoredObjects
-
- getObjectsRejected() - Method in class ObjectCollectionProviderFilterBase
-
- getObjectsSeeds() - Method in class SegmentChannel
-
- getObjectsSeeds() - Method in class SegmentWithSeeds
-
- getObjectsSource() - Method in class AssignFromIntersectingObjects
-
- getObjectsSource() - Method in class SegmentWithSeeds
-
- getObjectsSplitBy() - Method in class SplitByObjects
-
- getObjectsTarget() - Method in class AssignFromIntersectingObjects
-
- getOffByte() - Method in class Mask
-
- getOffByte() - Method in class BinaryValuesByte
-
The byte representation of the value for OFF
- getOffInt() - Method in class Mask
-
- getOffInt() - Method in class BinaryValues
-
The integer representation of the value for OFF
- getOnByte() - Method in class Mask
-
- getOnByte() - Method in class BinaryValuesByte
-
The byte representation of the value for ON
- getOnInt() - Method in class Mask
-
- getOnInt() - Method in class BinaryValues
-
The integer representation of the value for ON
- GetOperationFailedException - Exception in org.anchoranalysis.core.index
-
When a get operation fails for a particular key
- GetOperationFailedException(Exception) - Constructor for exception GetOperationFailedException
-
- GetOperationFailedException(int, String) - Constructor for exception GetOperationFailedException
-
- GetOperationFailedException(int, Throwable) - Constructor for exception GetOperationFailedException
-
- GetOperationFailedException(String, String) - Constructor for exception GetOperationFailedException
-
- GetOperationFailedException(String, Throwable) - Constructor for exception GetOperationFailedException
-
- getOptimization() - Method in class SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
- getOptional(String) - Method in interface NamedProvider
-
Retrieves the item if it exists, or returns empty() if it doesn't exist.
- getOptional(String) - Method in class NamedProviderBridge
-
- getOptional(String) - Method in class NamedProviderCombine
-
- getOptional(String) - Method in class NameValueSet
-
- getOptional(String) - Method in class EagerEvaluationStore
-
- getOptional(String) - Method in class LazyEvaluationStore
-
- getOptional(String) - Method in class SharedFeatureMulti
-
- getOptional(String) - Method in class NamedStacks
-
- getOptional(String) - Method in class WrapStackAsTimeSequence
-
- getOptional(String) - Method in class WrapStackAsTimeSequenceStore
-
- getOptional(String) - Method in class WrapTimeSequenceAsStack
-
- getOptionList() - Method in class KernelProposer
-
- getOptions() - Method in class BioformatsReader
-
Options that influence how stack is read.
- getOptions() - Method in class ReadOptionsDelegate
-
- getOrCalculate(T) - Method in class ResolvedCalculation
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from previously.
- getOrCalculate(T, U) - Method in class ResolvedCalculationMap
-
- getOrCalculate(T) - Method in class FeatureCalculation
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from previously.
- getOrCalculate(T, U) - Method in class FeatureCalculationMap
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from previously.
- getOrCreate(Class<?>) - Method in class SharedObjects
-
Gets an existing store, or creates a new one
- getOrCreateNew(K) - Method in class MapCreate
-
- getOrientation() - Method in class Ellipse
-
- getOrientation() - Method in class Ellipsoid
-
- getOrientationProposer() - Method in class OrientationAndRadiiProposer
-
- getOrientationXYProposer() - Method in class XYOrientationExtendToZ
-
- getOriginal() - Method in class OverlappingObject
-
Original unscaled element before any operations
- getOrNull(U) - Method in class FeatureCalculationMap
-
Gets an existing result for the current params from the cache.
- getOtherwise() - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is not selected.
- getOutlineColor() - Method in class SegmentInstanceWithModel
-
The color of the outline
- getOutlinePixelsRetriever() - Method in class TraversePointsOnContour
-
- getOutlinePixelsRetrieverReverse() - Method in class TraversePointsOnContour
-
- getOutlineWidth() - Method in class BoundingBoxOutline
-
- getOutlineWidth() - Method in class Outline
-
- getOutlineWidth() - Method in class CompareAnnotations
-
- getOutlineWidth() - Method in class AtScale
-
- getOutlineWidth() - Method in class ColoredBase
-
The width of the outline (only relevant if outline==true
- getOutlineWidth() - Method in class OutlinePreserveRelativeSize
-
The width of the outline.
- getOutlineWidth() - Method in class SegmentInstanceWithModel
-
The width of the outline
- getOutlineWidth() - Method in class VisualizeOnBackground
-
- getOutlineWidth() - Method in class ExportObjectsAsCroppedImages
-
- getOutPath() - Method in class InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- getOutput() - Method in class OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- getOutput() - Method in class ExperimentExecutor
-
- getOutput() - Method in class QuickMultiDatasetExperiment
-
- getOutputDirectory() - Method in class Outputter
-
- getOutputDirectory() - Method in class OutputterChecked
-
- getOutputDirectory() - Method in class OutputPrefixerSettings
-
A directory indicating where inputs can be located
- getOutputEnabledDelta() - Method in class OutputArguments
-
Additions/subtractions of outputs for the experiment supplied by the user.
- getOutputName() - Method in class ToTextFileBase
-
The name to use (without extension) for the text-file log
- getOutputName() - Method in class FeatureCSVMetadata
-
The output name for the features CSV.
- getOutputName() - Method in class OutputtedFile
-
- getOutputName() - Method in class OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- getOutputName() - Method in class PeriodicSubdirectoryReporter
-
- getOutputName() - Method in class MinimalExecutionTimeStatsReporter
-
- getOutputName() - Method in class VoxelizedMarksChangeReporter
-
- getOutputNameStyle() - Method in class OutputPattern
-
- getOutputNameStyle() - Method in class FromOutputName
-
- getOutputPattern() - Method in class BoundOutputter
-
- getOutputRGBOutline() - Method in class ExportObjectsAsCroppedImages
-
- getOutputRGBOutlineFlattened() - Method in class ExportObjectsAsCroppedImages
-
- getOutputsDisabled() - Method in class SpecificDisabled
-
The names of the outputs that are disbled.
- getOutputsEnabled() - Method in class SpecificEnabled
-
The names of the outputs that are enabled.
- getOutputsEnabled() - Method in class OutputManager
-
Which outputs are enabled or not enabled.
- getOutputsEnabled() - Method in class OutputterChecked
-
Which outputs are enabled or not enabled.
- getOutputsEnabled() - Method in class ElementOutputter
-
Which outputs are enabled or not enabled.
- getOutputStackProvider() - Method in class ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the
groupIdentifier.
- getOutputter() - Method in class InitializationContext
-
- getOutputter() - Method in class InputBound
-
- getOutputter() - Method in class InputOutputContextStateful
-
- getOutputter() - Method in class ParametersExperiment
-
- getOutputter() - Method in class BoundOutputter
-
The outputter to be used for the sequence.
- getOutputter() - Method in interface InputOutputContext
-
An outputter that writes to the particular output-directory.
- getOutputter() - Method in class ElementOutputter
-
The outputter for writing the element.
- getOutputter() - Method in class OptimizationContext
-
- getOutputterFor(String) - Method in class SharedStateFilteredImageOutput
-
groupIdentifierFor should always called at least once before getOutputManagerFor
- getOutputWriteSettings() - Method in class OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- getOutputWriteSettings() - Method in class QuickExperiment
-
- getOutside() - Method in class UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- getOutsideKernelPolicy() - Method in class KernelApplicationParameters
-
How to handle voxels that appear in a neighbourhood that lies outside the scene boundaries.
- getOverlapRatioThreshold() - Method in class KernelBirthAndKill
-
- getOverlapThreshold() - Method in class ConditionallyMergeOverlappingObjects
-
The maximum size for merging.
- getOverlays() - Method in class ColoredOverlayCollection
-
- getOverlays() - Method in class IndexableOverlays
-
- getPadding() - Method in class TextStyle
-
Padding added around the text in both dimensions if a default size is inferred (ignored if an
explicit size is specified )
- getPadding() - Method in class DrawCroppedObjectsGenerator
-
- getPadding() - Method in class ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- getPaddingXY() - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY
directions
- getPaddingZ() - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- getPair() - Method in class MergedPairsFeatures
-
- getPair() - Method in class EnergyPair
-
- getPair() - Method in class MarksWithEnergyBreakdown
-
Every combination of interactions between marks and the associated energy
- getPairAddCriteria() - Method in class EnergySchemeCreatorByElement
-
- getPairAddCriteria() - Method in class EnergyScheme
-
- getPairCollection() - Method in class KernelMerge
-
- getPairsFor(Mark) - Method in class RandomCollectionWithAddCriteria
-
- getPairTypeClass() - Method in class RandomCollectionWithAddCriteria
-
- getParametersExperiment() - Method in class ParametersUnbound
-
- getParamPrefix() - Method in class PermuteFeatureSequenceInteger
-
- getParams() - Method in class HOGDescriptor
-
Parameters used for calculating HOG
- getParams() - Method in class HOGFeature
-
Parameters used for calculating HOG
- getParamsOptional() - Method in class FeatureInputEnergy
-
- getParamsOptional() - Method in interface FeatureInputParams
-
- getParamsOptional() - Method in class FeatureInputMark
-
- getParamsRequired() - Method in interface FeatureInputParams
-
- getParent() - Method in class ErrorNodeImpl
-
- getParentDirectory() - Method in class MutableDirectory
-
- getParentDirectory() - Method in class OutputtedFile
-
- getParentDirectoryCreator() - Method in class OutputterTarget
-
- getParentOutputter() - Method in class PeriodicSubdirectoryReporter
-
- getPartition() - Method in class MarksFromPartition
-
- getPath() - Method in class AnnotationWithStrategy
-
Path to annotation
- getPath() - Method in class NotFound
-
the path an object was not found at.
- getPath() - Method in class RootPath
-
A path on a filesystem to the directory, that defines the root
- getPath() - Method in class SingleFile
-
- getPath() - Method in class NamedFile
-
- getPath() - Method in class NamedPath
-
The path
- getPath() - Method in class RootedFilePath
-
- getPath() - Method in class StaticFilePath
-
- getPath() - Method in class FileDetails
-
- getPathAnnotation() - Method in class SinglePathStrategy
-
- getPathDefaultMarks() - Method in class MarkProposerStrategy
-
- getPathLabel() - Method in class ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- getPathParams() - Method in class MarkProposerStrategy
-
- getPathParser() - Method in class GroupFiles
-
- getPaths() - Method in class InputArguments
-
A list of paths referring to specific inputs;
- getPaths() - Method in class FileSetFromStringSet
-
- getPaths() - Method in class FilterForExistingFiles
-
All files need to be present
- getPayload() - Method in class TypedEdge
-
The edge.
- getPayload() - Method in class ObjectVertex
-
- getPenaltyValue() - Method in class MaxOverlapRatio
-
- getPeriodTriggerBank() - Method in class FeedbackBeginParameters
-
- getPermutation() - Method in class PermuteFeature
-
A permutation to apply.
- getPermutations() - Method in class PermuteFeature
-
A list of permutations to apply.
- getPermuteProperty() - Method in class Permute
-
- getPermuteProperty() - Method in class PermuteFeatureSequenceInteger
-
- getPixelsForPlane(int) - Method in class EncodedVoxels
-
- getPlotBackgroundColor() - Method in class PlotColorScheme
-
- getPlotGridlineColor() - Method in class PlotColorScheme
-
- getPlusOne() - Method in class SlidingBuffer
-
The voxel-buffer for the slice with the currently selected slice's index +1 or null
if it's the final slice.
- getPoint() - Method in class KernelPointCursor
-
The point around which the cursor may iterate.
- getPointFitters() - Method in class PointsInitialization
-
- getPoints() - Method in class PointListBase
-
- getPoints() - Method in class Contour
-
- getPointsFitter() - Method in class CreateMarkFromPoints
-
- getPointsFitter() - Method in class MarkProposerStrategy
-
- getPointsFitter() - Method in class FitPoints
-
- getPointsFitter() - Method in class FitPointsFromObjects
-
- getPointsFitter() - Method in class PointsFitterToMark
-
- getPointsFitter() - Method in class ReflectInAxesWithinDistance
-
- getPointsFromOrientationProposer() - Method in class MergeLists
-
- getPointsFromOrientationXYProposer() - Method in class XYOrientationExtendToZ
-
- getPointsProposer() - Method in class FitPoints
-
- getPosition() - Method in class MarkWithPosition
-
- getPositionProposer() - Method in class Position
-
- getPositionProposer() - Method in class Repeat
-
- getPostcondition() - Method in class DilationContext
-
If defined, a condition which must be satisfied after an iteration occurs, otherwise
no more iterations occur.
- getPower() - Method in class MeanRaisedToPower
-
- getPredicates() - Method in class PathMatchConstraints
-
Predicates for both a file and a directory.
- getPrefix() - Method in class DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created
- getPrefix() - Method in class PermutePropertySequenceIntegerWithinString
-
- getPrefix() - Method in class PathPrefixerAvoidResolve
-
A string prefixed to each output-path.
- getPrefix() - Method in class OutputterTarget
-
- getPrefix() - Method in class Outputter
-
- getPrefix() - Method in class OutputterChecked
-
- getPrefix() - Method in class ExperimentStructure
-
- getPrefixer() - Method in class OutputArguments
-
Where outputs are written, and how identifiers are styled.
- getPrefixer() - Method in class ParametersExperiment
-
- getPrefixer() - Method in class OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- getPrefixer() - Method in class PathPrefixerContext
-
Settings for where and how outputs should be prefixed.
- getPrefixer() - Method in class LastDirectoryAsPrefix
-
- getPrefixer() - Method in class Rooted
-
- getPrefixerElse() - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is not true.
- getPrefixerIf() - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is true.
- getPrefixToRemove() - Method in class DirectoryStructure
-
- getPrependColor() - Method in class Prepend
-
- getPrependString() - Method in class ListSequence
-
- getPrependString() - Method in class PrependName
-
- getPrependString() - Method in class DeriveFromPair
-
- getPrependString() - Method in class FeatureListProviderAggregatePair
-
- getPriority() - Method in class PrioritisedVertex
-
- getProbNeg() - Method in class KernelPosNeg
-
- getProbPos() - Method in class KernelPosNeg
-
- getProgress() - Method in class InputManagerParams
-
- getProperties() - Method in class ObjectWithProperties
-
- getProperty(String) - Method in class ObjectWithProperties
-
- getPropertyDefiner() - Method in class InitializableBean
-
- getPropertyInitializer() - Method in class InitializableBean
-
- getPropertyPath() - Method in class PermutePropertyWithPath
-
Either a direct property of a bean e.g.
- getProposal() - Method in class OptimizationStep
-
- getProposal() - Method in class Reporting
-
- getProposalSecondary() - Method in class Reporting
-
An optional additional marks-Energy that provides an additional explanation of proposed
- getProposer() - Method in class MarkFromCollectionProposerUnary
-
- getProposer() - Method in class MarkProposerUnary
-
- getProvider() - Method in class FromProvider
-
- getPxlPartMemo() - Method in class FeatureInputAllMemo
-
- getPxlPartMemo() - Method in class FeatureInputSingleMemo
-
- getQuantile() - Method in class Quantile
-
The quantile.
- getQuantile() - Method in class QuantileStretch
-
- getQuantile() - Method in class Quantile
-
- getQuantile() - Method in class DiscardOutliers
-
- getQuantile() - Method in class Quantile
-
- getQuantile() - Method in class QuantileAcrossObjects
-
- getQuantile() - Method in class QuantileAcrossConnectedComponents
-
- getQuantileHigh() - Method in class Range
-
- getQuantileLow() - Method in class Range
-
- getQuantileLower() - Method in class ToByteUpperLowerQuantileIntensity
-
- getQuantileUpper() - Method in class ToByteUpperLowerQuantileIntensity
-
- getRadii() - Method in class Ellipse
-
- getRadii() - Method in class Ellipsoid
-
- getRadiiProposer() - Method in class OrientationAndRadiiProposer
-
- getRadiiProposer() - Method in class RadiiProposerRepeat
-
- getRadius() - Method in class MarkWithPositionAndSingleRadius
-
- getRadius() - Method in class AutoLocalThreshold
-
- getRadius() - Method in class WithRadiusBase
-
- getRadiusBound() - Method in class UniformRandomRadiiProposer
-
- getRadiusX() - Method in class FitResult
-
- getRadiusY() - Method in class FitResult
-
- getRadiusZ() - Method in class FitResult
-
- getRandomNumberGenerator() - Method in class ProposerContext
-
- getRangeAxisLimits() - Method in class PlotInstance
-
- getRangeC() - Method in class SizeExtents
-
- getRangeT() - Method in class SizeExtents
-
- getRangeZ() - Method in class SizeExtents
-
- getRate() - Method in class Geometry
-
- getRaw() - Method in class UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at the current buffer position.
- getRaw(int) - Method in class UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at a particular buffer position.
- getRaw() - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as an int) at the current buffer position.
- getRaw(int) - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a int) at a particular buffer position.
- getRaw() - Method in class UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at the current buffer position.
- getRaw(int) - Method in class UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at a particular buffer position.
- getReaderMatching() - Method in class BranchExtension
-
The reader to use if the extension matches.
- getReaderNotMatching() - Method in class BranchExtension
-
The reader to use if the extension does not match.
- getReason() - Method in class NotFound
-
- getReceive() - Method in class CombineBase
-
- getRecordedOutputs() - Method in class RecordedOutputsWithRules
-
If defined, records output-names that are written / not-written during the experiment.
- getRed() - Method in class RGBColorBean
-
- getRed() - Method in class RGBColor
-
- getRed() - Method in class ThreeChannels
-
- getReduce() - Method in class FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- getReduce() - Method in class SuppressNonMaxima
-
The algorithm for reducing the number of object-masks.
- getReferencePoissonIntensity() - Method in class MarkWithIdentifierFactory
-
- getReferencesFeatureListCreator() - Method in class ReferencedFeatures
-
Ensures any feature-lists mentioned here are evaluated, before this list is created.
- getReferencesFeatureListCreator() - Method in class PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- getRegex() - Method in class RegularExpressionBase
-
- getRegEx() - Method in class RegExMatcher
-
- getRegEx() - Method in class PathRegEx
-
Regular expression to use to match path with at least one group in it.
- getRegEx() - Method in class RemoveMatching
-
If a path matches a regular expression it is removed.
- getRegEx() - Method in class Exclude
-
- getRegEx() - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups.
- getRegEx() - Method in class JoinRegExGroups
-
- getRegex() - Method in class Replace
-
Regular expression to match against string
- getRegex() - Method in class QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- getRegEx() - Method in class ExperimentStructure
-
- getRegexAdjacent() - Method in class NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- getRegExDir() - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to directories
- getRegExFile() - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to files
- getRegion() - Method in class Thresholded
-
- getRegion() - Method in class Intensity
-
- getRegionID() - Method in class RegionMembershipWithFlags
-
- getRegionID() - Method in class VolumeMin
-
- getRegionID() - Method in class FromMarks
-
- getRegionID() - Method in class IndexedRegionBase
-
- getRegionID() - Method in class ColoredMarks
-
- getRegionID() - Method in class FeatureMarkRegion
-
- getRegionID() - Method in class FeatureSingleMemoRegion
-
- getRegionID() - Method in class FeaturePairMemoSingleRegion
-
- getRegionID() - Method in class KernelBirthAndKill
-
- getRegionMap() - Method in class EnergySchemeCreatorByElement
-
- getRegionMap() - Method in class EnergyScheme
-
- getRegionMap() - Method in class EnergySchemeWithSharedFeatures
-
- getRegionMap() - Method in class EnergyMemoList
-
- getRegionMap() - Method in class VoxelizedMarkMemo
-
- getRegionMap() - Method in class ProposerContext
-
- getRegionMap() - Method in class FromMarks
-
- getRegionMap() - Method in class AsObject
-
- getRegionMap() - Method in class SurfaceSizeMaskNonZero
-
- getRegionMembership() - Method in class RegionMembershipWithFlags
-
- getRejectionReason() - Method in class DualMarksAnnotation
-
- getRelation() - Method in class RelationToConstant
-
- getRelation() - Method in class ObjectFilterRelation
-
- getRelation() - Method in class MergePairs
-
Relation to threshold
- getRelation() - Method in class IdentityImposeValueRelationToHistogram
-
- getRelation() - Method in class RejectIfConditionXYResolution
-
A predicate defined by the relationship of the XY-resolution to a constant threshold.
- getRelation() - Method in class AddCriteriaFeatureRelationThreshold
-
- getRelation() - Method in class RequireFeatureRelationThreshold
-
- getRemainder() - Method in class SplitPath
-
- getRepeat() - Method in class MovieFromSlices
-
- getRepeats() - Method in class KernelBirth
-
Total number of births
- getRepeatZProvider() - Method in class GenerateString
-
Repeats the generated (2D) string in z, so it's the same z-extent as repeatZProvider
- getReplacement() - Method in class SubstituteRegularExpression
-
- getReplacement() - Method in class Replace
-
What to replace in the path
- getReplacement() - Method in class AdjacentFile
-
The replacement string used to determine the file
- getRequireArguments() - Method in class OnlyIf
-
The conditions that must be fulfilled
- getRequireArguments() - Method in class FeedbackReceiverRequireArguments
-
- getResizeTo() - Method in class GroupedMeanChannelTask
-
If set, each channel is scaled to a specific size before the mean is calculated (useful for
combining different sized images)
- getResizeTo() - Method in class HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- getResizeTo() - Method in class HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors
- getResolution() - Method in class BinarySegmentationParameters
-
- getResolutionOptional() - Method in class FeatureInputEnergy
-
- getResolutionOptional() - Method in interface FeatureInputWithResolution
-
- getResolutionOptional() - Method in class FeatureInputHistogram
-
- getResolutionOptional() - Method in class FeatureInputMarkCollection
-
- getResolutionOptional() - Method in class FeatureInputMark
-
- getResolutionRequired() - Method in interface FeatureInputWithResolution
-
- getRestrictTo() - Method in class Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this
mask
- getResults() - Method in class FeatureInputResults
-
- getResultsVector() - Method in class ResultsVectorWithThumbnail
-
- getRGB() - Method in class RGBColorBean
-
- getRGB() - Method in class RGBColor
-
- getRight() - Method in class ObjectsToCompare
-
Objects on right-side of the comparison
- getRoot() - Method in class SplitPath
-
- getRoot() - Method in class ProposerFailureDescription
-
- getRoot() - Method in class TestLoader
-
- getRoot1() - Method in class QuadraticEquationSolver.QuadraticRoots
-
- getRoot2() - Method in class QuadraticEquationSolver.QuadraticRoots
-
- getRootDirectory() - Method in class Manifest
-
- getRootName() - Method in class Rooted
-
The name of the root-path to associate with this fileset.
- getRootName() - Method in class RootedFilePath
-
- getRootName() - Method in class Rooted
-
- getRootName() - Method in class Rooted
-
- getRootName() - Method in class QuickBase
-
If non-empty then a rooted filesystem is used with this root
- getRootName() - Method in class RootedExperiment
-
Root-name assuming multi-rooted structure.
- getRootNameForStructure() - Method in class ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- getRootPath() - Method in class DeserializedManifest
-
- getRotationAngle() - Method in class BoundRotation2D
-
- getRotationMatrix() - Method in class OrientationRotationMatrix
-
- getRotationX() - Method in class BoundRotation3D
-
- getRotationY() - Method in class BoundRotation3D
-
- getRotationZ() - Method in class BoundRotation3D
-
- getRotMatrix() - Method in class FitResult
-
- getRow(int) - Method in class TableItemArrangement
-
- getRow() - Method in class Cell
-
- getRowForListIndex(int) - Method in class TableItemArrangement
-
- getRowSource() - Method in class InputProcessContext
-
- getSampleEvery() - Method in class SampleWithDirectory
-
- getScalarProposer() - Method in class MaxWithConstant
-
- getScalarProposer() - Method in class Scale
-
- getScale() - Method in class FirstSecondOrderStatistic
-
Standard-Deviation
- getScale() - Method in class MontageSlices
-
Whether to increase or reduce the size of the images
- getScaleCalculator() - Method in class ScaleXY
-
- getScaleCalculator() - Method in class ScaleXY
-
Determines how much to scale by
- getScaleCalculator() - Method in class Scale
-
- getScaleCalculator() - Method in class AtScale
-
- getScaleCalculator() - Method in class Invert
-
- getScaleCalculator() - Method in class ScaleImage
-
Calculates what scale-factor to apply on the image.
- getScaleCalculator() - Method in class ScaleXY
-
- getScaleFactor() - Method in class GradientBase
-
- getScaleInput() - Method in class SegmentObjectsFromTensorFlowModel
-
Any scaling to be applied to the input-image before being input to the model for inference.
- getScaleLower() - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- getScaleLower() - Method in class ScaleByParams
-
- getScaleRadii() - Method in class ConicFitterBase
-
- getScaleUpper() - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- getScaleUpper() - Method in class ScaleByParams
-
- getScore() - Method in class ScoreVoxels
-
- getScoreExtracter() - Method in class AcceptanceProbabilityCalculator
-
- getScoreProvider() - Method in class ExtractSlice
-
- getScoreThreshold() - Method in class RemoveOverlappingObjects
-
Bounding boxes with scores above this threshold are removed
- getSearchObjects() - Method in class FeatureIntersectingObjects
-
- getSecond() - Method in class CostMatrix
-
- getSecond() - Method in class FeatureInputPairObjects
-
- getSecond() - Method in class OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names)
- getSecond() - Method in class Compose
-
Second transformation from U to T
- getSecondary() - Method in class StateReporterToPixelized
-
- getSegment() - Method in class BinarySegmentationOne
-
- getSegment() - Method in class SegmentChannelIntoObjectsUnary
-
- getSegment() - Method in class SegmentChannel
-
Segmentation algorithm
- getSegment() - Method in class SegmentChannel
-
- getSegment() - Method in class SegmentChannelByObject
-
- getSegment() - Method in class SegmentStack
-
The segmentation procedure.
- getSegment() - Method in class SegmentWithSeeds
-
- getSegment() - Method in class ConnectedComponentsFromBinarySegmentation
-
- getSegment() - Method in class SegmentInstanceWithModel
-
The segmentation algorithm
- getSegment() - Method in class SegmentMarksFromImage
-
How to perform the segmentation.
- getSegment() - Method in class SuppressNonMaxima
-
The segmentation algorithm that is applied as an input to non-maxima suppression.
- getSegmentStack() - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- getSelect() - Method in class DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- getSelectChannels() - Method in class GroupedStackBase
-
Selects which channels are included, optionally renaming.
- getSemiMajorAxis() - Method in class EllipseStandardFormConverter
-
- getSemiMinorAxis() - Method in class EllipseStandardFormConverter
-
- getSeperator() - Method in class ListSequence
-
- getSeperator() - Method in class CombineCSV
-
- getSequence() - Method in class PermutePropertySequence
-
Where the sequence starts
- getSequence() - Method in class ListSequence
-
First number range that is appended
- getSequence() - Method in class ChangeableOutputSequence
-
- getSequenceAdditional() - Method in class ListSequence
-
Another number range that is appended
- getSequenceType() - Method in class OutputSequenceIndexed
-
- getSequenceType() - Method in class ManifestDirectoryDescription
-
A sequence-type to describe the different filenames outputted in the directory.
- getSeriesColors() - Method in class PlotIndexBaseCategorical
-
- getSeriesNameFor(int) - Method in class PlotIndexBase
-
- getSet() - Method in class SharedFeatureSet
-
- getSettings() - Method in class Outputter
-
- getSettings() - Method in class OutputterChecked
-
General settings for outputting.
- getSettings() - Method in class OutputWriteContext
-
User-define settings for outputting in output-manager.
- getSettings() - Method in class ElementOutputter
-
General settings for outputting.
- getSharedFeatures() - Method in class FeaturesInitialization
-
- getSharedFeatures() - Method in class EnergySchemeSet
-
- getSharedFeatures() - Method in class EnergySchemeWithSharedFeatures
-
- getSharedObjects() - Method in class FeatureInitialization
-
- getSharedObjects() - Method in class ImageInitialization
-
- getSharedState() - Method in class InputBound
-
- getSharedState() - Method in class ParametersUnbound
-
- getSharedState() - Method in class CopyContext
-
State shared across all inputs when copying.
- getSharedState() - Method in class SharedStateRememberConverted
-
The shared state.
- getShellRad() - Method in class MarkEllipseFactory
-
- getShellRad() - Method in class MarkEllipsoidFactory
-
- getShellRad() - Method in class Ellipse
-
- getShellRad() - Method in class Ellipsoid
-
- getShellRad() - Method in class FromObjects
-
- getShellRad() - Method in class CreateEllipse
-
- getShellRad() - Method in class ConicFitterBase
-
- getShortTitle() - Method in class Plot
-
- getShowOngoingJobsLessThan() - Method in class ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- getSigma() - Method in class BlurStrategy
-
- getSigma() - Method in class GaussianBlur2D
-
- getSimplePairCollectionID() - Method in class KernelMerge
-
- getSingle() - Method in class MergedPairsFeatures
-
- getSize() - Method in class TaskArguments
-
Suggests dimensions or a scaling-factor to resize an image to.
- getSize() - Method in class TextStyle
-
Explicit size of the image the string is draw on
- getSize() - Method in class Kernel
-
- getSize() - Method in class Aggregator
-
- getSize() - Method in class PlotHistogram
-
Size of the image produced showing a plot of the histogram
- getSize() - Method in class OutlinePreserveRelativeSize
-
Size of all created thumbnails
- getSize() - Method in class ScaleToSize
-
- getSize() - Method in class MovieFromSlices
-
- getSize() - Method in class IntegerRange
-
- getSizeHalf() - Method in class Kernel
-
- getSizeXY() - Method in class SpecifyDimensions
-
Length of X and Y dimensions.
- getSizeZ() - Method in class SpecifyDimensions
-
Length of Z dimension.
- getSkipFirstTrim() - Method in class RemoveTrailingDirectory
-
- getSkipFirstTrim() - Method in class FilePathAppendBase
-
- getSkipNumberSubdirectories() - Method in class LastDirectories
-
Initially skip this number of directories before including them in the description.
- getSlice(int) - Method in interface VoxelPartition
-
- getSlice(int) - Method in class VoxelPartitionHistogram
-
- getSlice() - Method in class RepeatSlice
-
- getSliceFirst() - Method in class MontageSlices
-
First slice.
- getSliceID() - Method in class SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- getSliceIndex() - Method in class RepeatSlice
-
Which slice to use from mask
- getSliceIndex() - Method in class FileDetails
-
- getSliceLast() - Method in class MontageSlices
-
Last slice.
- getSmoothingFactor() - Method in class SplitContourAtSaddlePoints
-
- getSource() - Method in class StringMapItem
-
- getSource() - Method in class MatchedObject
-
The source object (which is matched against others)
- getSource() - Method in class IdentifiablePair
-
- getSource() - Method in class PairPxlMarkMemo
-
- getSource() - Method in class ExportFeatures
-
Source of feature-values to be exported
- getSource() - Method in class DualVoxelizedMarks
-
- getSource() - Method in class ToPixelized
-
- getSourceDirectory() - Method in class CopyContext
-
Source directory of copying.
- getSplitDescriptiveNameRegex() - Method in class CompareAnnotations
-
- getSplitProposer() - Method in class KernelSplit
-
- getSquareSize() - Method in class SplitIntoSquares
-
- getStack() - Method in class StackProviderUnary
-
- getStack() - Method in class DisplayStack
-
- getStack() - Method in class StackProviderWithLabel
-
- getStack() - Method in class ColoredMarksWithDisplayStack
-
- getStack() - Method in class MarksWithDisplayStack
-
- getStack() - Method in class FromStack
-
Provides a stack.
- getStack() - Method in class SegmentStack
-
The stack to segment
- getStack() - Method in class ExportObjectsFromCSV
-
The stack that is the background for our objects
- getStackEnergy() - Method in class FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- getStackEnergy() - Method in class FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is
considered to be the input stacks)
- getStackEnergy() - Method in class BinaryClassifierImageLabeller
-
- getStackEnergy() - Method in class ExtractSlice
-
- getStackEnergy() - Method in class DefineOutputterWithEnergy
-
- getStackID() - Method in class IfStackExists
-
- getStackName() - Method in class One
-
If defined, processing only occurs the stack with this specific stack and index.
- getStackNameVisualOriginal() - Method in class AnnotationBackground
-
- getStackProviderID() - Method in class FromStack
-
Specifies the ID of an existing stack.
- getStackProviderID() - Method in class FromStackChannel
-
- getStackReader() - Method in class AnnotatorStrategy
-
- getStackReader() - Method in class InputManagerWithStackReader
-
- getStackReader() - Method in class MaskComparer
-
- getStackReader() - Method in class AnnotationComparisonInput
-
- getStackReader() - Method in class FlattenAsChannel
-
Reads the image that is subsequently flattened.
- getStackReader() - Method in class ImposeResolution
-
Reads an image before a resolution is imposed.
- getStackReader() - Method in class MultiFileReader
-
- getStackReader() - Method in class ReadVoxelExtentXml
-
Reads an image before a resolution is imposed.
- getStackReader() - Method in class RejectIfConditionXYResolution
-
Reads an image before a resolution is imposed.
- getStackReaderAdjacent() - Method in class NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- getStackReaderAppend() - Method in class QuickBase
-
The raster-reader for reading any appended files
- getStackStore() - Method in class ChannelSource
-
- getStart() - Method in class SequenceInteger
-
The index to begin iteration from
- getStartIndex() - Method in class IndexRange
-
The index if the first element to use in the subsetting range, zero-indexed.
- getStartIndex() - Method in class MovieFromSlices
-
- getStartingIntensity() - Method in class FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- getStartPoint() - Method in class LineSegment
-
- getState() - Method in class FeedbackEndParameters
-
- getStateReporter() - Method in class TransformationAssignMode
-
- getStrategy() - Method in class AnnotationWithStrategy
-
- getStrategy() - Method in class BoundReplaceStrategy
-
- getStrategy() - Method in class Blur
-
- getStringRasterGenerator() - Method in class GenerateString
-
- getSubdirectory() - Method in class AppendDictionary
-
- getSubdirectory() - Method in class ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix
${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- getSubdirectoryName() - Method in class OutputPattern
-
The name of a subdirectory in the current context to write to, or if empty, files are written
into the current directory context.
- getSubtractConstant() - Method in class IntensityGradientBase
-
- getSubtractRadii() - Method in class ConicFitterBase
-
- getSuffix() - Method in class PermutePropertySequenceIntegerWithinString
-
- getSuggestedFormatToWrite() - Method in class StackWriteOptions
-
A suggestion on what file-format to write.
- getSuggestedFormatToWrite() - Method in class OutputWriteContext
-
A suggestion on what file-format to write.
- getSuggestedFormatToWrite() - Method in class ElementOutputter
-
- getSuggestedImageOutputFormat() - Method in class OutputPrefixerSettings
-
A file format suggested for writing images to the file system.
- getSuggestedResize() - Method in class InitializationContext
-
A suggested input on how to resize an image, if one is provided.
- getSuggestedResize() - Method in class ImageInitialization
-
- getSum() - Method in class RunningSum
-
The running sum
- getSummarizer() - Method in class SummarizerInputFromManager
-
- getSummarizer() - Method in class SummarizeBase
-
- getSummarizerElse() - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) <= countThreshold
- getSummarizerGreaterThan() - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) > countThreshold
- getTarget() - Method in class StringMapItem
-
- getTask() - Method in class JobProcessor
-
- getTask() - Method in class ExperimentExecutor
-
- getTask() - Method in class ConvertNamedChannels
-
The underlying task that will be called, perhaps with a different input-type.
- getTask() - Method in class QuickExperiment
-
- getTask() - Method in class QuickMultiDatasetExperiment
-
- getTask() - Method in class QuickMultiDatasetStructuredExperiment
-
- getTaskArguments() - Method in class InputBound
-
- getTaskName() - Method in class TaskArguments
-
A name to describe the ongoing task.
- getTaskProcessor() - Method in class InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- getTemperature() - Method in class Aggregator
-
- getTemperature() - Method in class Reporting
-
- getTemplateMark() - Method in class MarkWithIdentifierFactory
-
- getTemporary() - Method in class EncodedVoxels
-
- GetterFromIndex<T> - Interface in org.anchoranalysis.core.index
-
- getTermination() - Method in class SimulatedAnnealing
-
- getText() - Method in class GenerateString
-
Text to draw on an image
- getThreshold() - Method in class RelationToConstant
-
- getThreshold() - Method in class CutBelowThreshold
-
- getThreshold() - Method in class CalculateLevelRelativeToThreshold
-
- getThreshold() - Method in class IntensityGreaterEqualThan
-
- getThreshold() - Method in class ThresholdedFeature
-
- getThreshold() - Method in class ThresholdedVolume
-
- getThreshold() - Method in class Count
-
- getThreshold() - Method in class RatioThreshold
-
- getThreshold() - Method in class FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- getThreshold() - Method in class AddCriteriaFeatureRelationThreshold
-
- getThreshold() - Method in class RequireFeatureRelationThreshold
-
- getThreshold() - Method in class GreatestAreaSlice
-
- getThreshold() - Method in class Thresholded
-
- getThreshold() - Method in class IfCondition
-
- getThresholder() - Method in class BinarySegmentationThreshold
-
- getThresholder() - Method in class Threshold
-
The thresholder that will convert a channel into a binary-channel
- getThumbnail() - Method in class CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more objects combine, as form a single input
- getThumbnail() - Method in class FromImage
-
Method to generate a thumbnail for images
- getThumbnail() - Method in class ResultsVectorWithThumbnail
-
- getThumbnailBatch() - Method in class ListWithThumbnails
-
- getTime() - Method in class JobState
-
- getTimeAnnotationLastUpdated() - Method in class DualMarksAnnotation
-
Number of seconds since the UNIX epoch
- getTimeIndex() - Method in class ConvertNamedChannelsToStack
-
- getTimeIndex() - Method in class FileDetails
-
- getTimeIndexGroupID() - Method in class RegularExpression
-
- getTimes() - Method in class Repeat
-
- getTitle() - Method in class ReportFeatureEvaluator
-
- getTitle() - Method in class Plot
-
The full title of the plot.
- getTitle() - Method in class ReportFeatureForManifestFileBase
-
- getTo() - Method in class TypedEdge
-
The vertex the edge joins to.
- getTolerance() - Method in class UnchangedScore
-
An exponent of 10 which determines a tolerance, less than which a score will be deemed
unchanged compared to another.
- getTotal() - Method in class EnergyTotal
-
- getTotalCount() - Method in class Histogram
-
- getTotalNumberTasks() - Method in class ConcurrentJobMonitor
-
- getTransformer() - Method in class RemovePartitionAndThen
-
- getTransformer() - Method in class VoxelizeWithTransform
-
- getTransformer() - Method in class KernelStateBridgePixelize
-
- getTransformerKernelToState() - Method in class KernelStateBridgeTransformer
-
- getTransformerMarks() - Method in class AddDualTransformer
-
- getTransformerPrimary() - Method in class StateReporterTransformer
-
- getTransformerSecondary() - Method in class StateReporterTransformer
-
- getTransformerStateToKernel() - Method in class KernelStateBridgeTransformer
-
- getTriggerTerminationCondition() - Method in class OptimizationContext
-
- getTrimTrailingDirectory() - Method in class RemoveTrailingDirectory
-
- getTrimTrailingDirectory() - Method in class FilePathAppendBase
-
- getType() - Method in class ManifestDescription
-
Identifies the type of entity.
- getUnconvertedVoxelAt(int, Point3i) - Method in class DisplayStack
-
- getUniqueLabel() - Method in class AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- getUnit() - Method in class BoundingBoxExtent
-
- getUnit() - Method in class FeatureSingleMemoRegion
-
- getUnitConverterOptional() - Method in class FeatureInputEnergy
-
- getUnitType() - Method in class DistancePhysical
-
- getUnitType() - Method in class AreaPhysical
-
- getUnitType() - Method in class VolumePhysical
-
- getUnitType() - Method in class FeatureConvertUnits
-
- getUnitType() - Method in class UnitConverter
-
- getUnitTypeFrom() - Method in class ConvertUnits
-
- getUnitTypeTo() - Method in class ConvertUnits
-
- getUnitValueDistance() - Method in class FromUnitValueDistance
-
- getUnsigned() - Method in class UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at the current buffer position.
- getUnsigned(int) - Method in class UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at a particular buffer position.
- getUnsigned() - Method in class UnsignedByteBuffer
-
- getUnsigned(int) - Method in class UnsignedByteBuffer
-
- getUnsigned() - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at the current buffer position.
- getUnsigned(int) - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at a particular buffer position.
- getUnsigned() - Method in class UnsignedShortBuffer
-
- getUnsigned(int) - Method in class UnsignedShortBuffer
-
- getUnsignedByte() - Static method in class VoxelsFactory
-
- getUnsignedInt() - Static method in class VoxelsFactory
-
- getUnsignedShort() - Static method in class VoxelsFactory
-
- getUserFriendlyLabel() - Method in class AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- getValue() - Method in class NamedBean
-
- getValue() - Method in interface NameValue
-
The associated value
- getValue() - Method in class SimpleNameValue
-
- getValue() - Method in class TypedValue
-
- getValue() - Method in class Constant
-
- getValue() - Method in class DistancePhysical
-
- getValue() - Method in class DistanceVoxels
-
- getValue() - Method in class UnitValueArea
-
- getValue() - Method in class VolumePhysical
-
- getValue() - Method in class VolumeVoxels
-
- getValue() - Method in class OptionalNameValue
-
The value.
- getValue() - Method in class AssignValue
-
- getValue() - Method in class CreateNew
-
- getValue() - Method in class UnaryWithValueBase
-
- getValue() - Method in class EmptyHistogramConstant
-
- getValue() - Method in class IfParamEqual
-
- getValue() - Method in class DictionaryCondition
-
The value the key should have in the dictionary, in order for the condition to be fulfilled.
- getValue() - Method in class ConstantScaleFactor
-
- getValue() - Method in class CountEqual
-
- getValue() - Method in class IdentityImposeValueRelationToHistogram
-
- getValue() - Method in class NormalizeByConstant
-
- getValue() - Method in class Constant
-
- getValue() - Method in class Constant
-
- getValue() - Method in class WithValueBase
-
- getValueIfEmpty() - Method in class FeatureHistogramStatistic
-
The value to return iff exceptionifEmpty is false
- getValueIfTooFewVoxels() - Method in class ImageMomentsBase
-
A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate
moments
- getValueNoObject() - Method in class ScoreObjects
-
- getValueNoObjects() - Method in class FeatureIntersectingObjects
-
- getValues() - Method in class PermutePropertyDoubleSet
-
- getValues() - Method in class PermutePropertyStringSet
-
The values of the string-set
- getVersion() - Method in class ExperimentIdentifierConstant
-
- getVertex() - Method in class PrioritisedVertex
-
- getVerticalAlign() - Method in class Overlay
-
- getVisitScheduler() - Method in class TraverseOutlineOnImage
-
- getVoxelDataType() - Method in class Channel
-
- getVoxelDataType() - Method in class VoxelsWrapper
-
- getVoxels() - Method in class SlidingBuffer
-
The voxels from which buffers corresponding to slices are extracted.
- getVoxelsConverter() - Method in class MaxIntensity
-
- getVoxelsConverter() - Method in interface ChannelConverterAttached
-
- getVoxelsConverter() - Method in class MaxIntensityFromHistogram
-
- getVoxelsConverter() - Method in class QuantileIntensityFromHistogram
-
- getVoxelsConverter() - Method in class UpperLowerQuantileIntensityFromHistogram
-
- getVoxelsConverter() - Method in class ChannelConverter
-
- getWeight() - Method in class WeightedKernel
-
- getWeight() - Method in class KernelProposerOptionSingle
-
- getWeightBackground() - Method in class OtsuWeighted
-
- getWeightedKernelFactory(int) - Method in class KernelProposer
-
- getWeightForeground() - Method in class OtsuWeighted
-
- getWeightItem1Greater() - Method in class Range
-
- getWeightItem2Greater() - Method in class Range
-
- getWeightNegative() - Method in class KernelProposerOption
-
- getWeightNegative() - Method in class KernelProposerOptionDual
-
- getWeightNegative() - Method in class KernelProposerOptionSingle
-
- getWeightPositive() - Method in class KernelProposerOption
-
- getWeightPositive() - Method in class KernelProposerOptionDual
-
- getWeightPositive() - Method in class KernelProposerOptionSingle
-
- getWeightWidthDescription() - Method in class WholeImageLabelStrategy
-
- getWhenBinaryChannel() - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled binary image.
- getWhenDetailed() - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- getWhenEqual() - Method in class IfParamEqual
-
- getWhenFalse() - Method in class IfElse
-
- getWhenNot() - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- getWhenNotEqual() - Method in class IfParamEqual
-
- getWhenRelative() - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is selected.
- getWhenRGB() - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled RGB image.
- getWhenSingleChannel() - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
- getWhenThreeChannels() - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled non-RGB image.
- getWhenTrue() - Method in class IfElse
-
- getWidth() - Method in class SizeXY
-
Size in X dimension.
- getWidth() - Method in class Difference
-
Width (what the difference is divided by)
- getWidth() - Method in class ImposeResolution
-
Physical pixel size of a voxel in x-dimension.
- getWidthFactor() - Method in class DifferenceCalculateLevelStandardDeviation
-
- getWindowSize() - Method in class CenterSliceWindow
-
- getWindowSize() - Method in class HOGParameters
-
The window-size as per OpenCV implementation.
- getWithConfidence() - Method in class LabelledWithConfidence
-
The element with associated confidence.
- getWithin() - Method in class UnitsWithinRange
-
Returned as a constant if a value lies within the range
- getWithinValue() - Method in class CompareWithRange
-
Constant to return if value lies within the range
- getWithinValue() - Method in class CompareWithRangeFeature
-
Constant to return if value lies within the range
- getWriter() - Method in class Flatten
-
- getWriter() - Method in class TextFileOutput
-
- getWriter() - Method in class BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- getWriter() - Method in class WriteResolutionXml
-
- getWriterAlways2D() - Method in class BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- getWriterElse() - Method in class BranchStack
-
Otherwise the writer to use.
- getWriterIfNoSuggestion() - Method in class BranchSuggestedFormat
-
The writer to use if there is no suggested file-format.
- getWriterInstance(Class<?>) - Method in class OutputWriteSettings
-
Gets a writer-instance for a particular writerParentClass.
- getWriters() - Method in class OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
- getWriters() - Method in class OutputterChecked
-
The writers associated with this output-manager.
- getWritersIfSuggested() - Method in class BranchSuggestedFormat
-
A list of writers to select if a given format is used
- getX() - Method in class VectorInDirection
-
- getX() - Method in class PlotAxisLabels
-
- getXDiv() - Method in class Orientation
-
- getXmlAggregatedGroup() - Method in class ResultsWriterOutputNames
-
The name of the XML file outputted with aggregated values for each group, if enabled.
- getXMLConfiguration() - Method in class Experiment
-
- getY() - Method in class VectorInDirection
-
- getY() - Method in class PlotAxisLabels
-
- getYAxisLowerMargin() - Method in class LinePlot
-
- getYAxisUpperMargin() - Method in class LinePlot
-
- getYVal(T, int) - Method in interface LinePlot.YValGetter
-
- getYValGetter() - Method in class BarPlot
-
- getYValGetter() - Method in class LinePlot
-
- getZ() - Method in class VectorInDirection
-
- getZAlign() - Method in class Overlay
-
- getZSliceGroupID() - Method in class RegularExpression
-
- getZSliceNum() - Method in class SortedSetSlice
-
- GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
-
- GlobExtractor - Class in org.anchoranalysis.io.input.path
-
Extracts a glob from a string describing it, and a direcory which gives it context.
- GlobExtractor.GlobWithDirectory - Class in org.anchoranalysis.io.input.path
-
- GlobWithDirectory(Optional<String>, String) - Constructor for class GlobExtractor.GlobWithDirectory
-
- GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
- GradientBase() - Constructor for class GradientBase
-
- GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
- GradientBaseAddSum() - Constructor for class GradientBaseAddSum
-
- gradientCalculation() - Method in class IntensityGradientBase
-
- GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Extracts the gradient in the direction of a particular axis (identified by an index)
- GradientForAxis() - Constructor for class GradientForAxis
-
- GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
- GradientMagnitude() - Constructor for class GradientMagnitude
-
- GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
- GradientMeanForAxis() - Constructor for class GradientMeanForAxis
-
- GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Gradient in x and y axes
- GradientXY() - Constructor for class GradientXY
-
- GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
-
- GraphLogger(DescribeGraph, Logger) - Constructor for class GraphLogger
-
- GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, where edges contain no payload.
- GraphWithoutPayload(boolean) - Constructor for class GraphWithoutPayload
-
Creates the graph.
- GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, with edges containing a payload of type E.
- GraphWithPayload(boolean) - Constructor for class GraphWithPayload
-
Creates the graph.
- GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
-
- GrayscaleReconstruction2DIJ() - Constructor for class GrayscaleReconstruction2DIJ
-
- GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- GrayscaleReconstructionByErosion() - Constructor for class GrayscaleReconstructionByErosion
-
- GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- GrayscaleReconstructionRobinson() - Constructor for class GrayscaleReconstructionRobinson
-
- greaterEqualThan(VarianceCalculator) - Method in class VarianceCalculator
-
- GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than
objectsLesser
- GreaterIntersectionWith() - Constructor for class GreaterIntersectionWith
-
- GreaterThan - Class in org.anchoranalysis.math.relation
-
- GreaterThan() - Constructor for class GreaterThan
-
- GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation
-
- GreaterThanBean() - Constructor for class GreaterThanBean
-
- GreaterThanEqualTo - Class in org.anchoranalysis.math.relation
-
- GreaterThanEqualTo() - Constructor for class GreaterThanEqualTo
-
- GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
-
- GreaterThanEqualToBean() - Constructor for class GreaterThanEqualToBean
-
- GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the
threshold
- GreaterThanThreshold() - Constructor for class GreaterThanThreshold
-
- GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- GreatestAreaSlice() - Constructor for class GreatestAreaSlice
-
- greedyMatch() - Method in class HungarianAlgorithm
-
Find a valid matching by greedily selecting among zero-cost matchings.
- GREEN - Static variable in class RGBChannelNames
-
Name for the green channel.
- green() - Method in class RGBStack
-
- GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label
-
A set of annotation labels partitoned into their unique groups
- GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class GroupedAnnotationLabels
-
- groupedLabels() - Method in class WholeImageLabelStrategy
-
- GroupedMeanChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.grouped.raster
-
Creates a an aggregated-image for each group, where each voxel-value is the mean voxel-value
across the group.
- GroupedMeanChannelTask() - Constructor for class GroupedMeanChannelTask
-
- GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Commonality between shared state for gouped export tasks
- GroupedSharedState(Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class GroupedSharedState
-
- GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped
-
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
- GroupedStackBase() - Constructor for class GroupedStackBase
-
- GroupFiles - Class in org.anchoranalysis.plugin.io.bean.file.group
-
An input-manager that can group together files to form stacks or time-series based on finding
patterns in the file path (via regular expressions)
- GroupFiles() - Constructor for class GroupFiles
-
- groupForKey(String) - Method in class AnnotationComparisonAssigner
-
- groupForKey(String) - Method in class FeatureCostAssigner
-
- groupForKey(String) - Method in class MaskIntersectionAssigner
-
- GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a set of definitions of classes can be collectively grouped using this class.
- GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Adds items to aggregate structures identified uniquely by a name, and allows these items to be
later outputted.
- GroupMapByName(String, String, Supplier<T>) - Constructor for class GroupMapByName
-
Creates a group-map.
- groupNameSet() - Method in class IndexedCSVRows
-
- GroupWriter - Class in org.anchoranalysis.feature.io.results.group
-
Writes outputs pertaining to groups to the filesystem.
- GroupWriter(ResultsWriterMetadata) - Constructor for class GroupWriter
-
- growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
Grows buffer of the object-mask in positive and negative directions by a certain amount.
- growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class ObjectMask
-
- growBy(Tuple3i, Extent) - Method in class BoundingBox
-
- growBy(int) - Method in class Extent
-
- growBy(ReadableTuple3i) - Method in class Extent
-
- growToZ(int) - Method in interface Seed
-
- growToZ(int) - Method in class SeedCollection
-
- growToZ(int) - Method in class SeedObjectMask
-
- growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
- growToZ(int) - Method in class ObjectMask
-
- guaranteedImageAttributes() - Method in class AssignmentGenerator
-
- guaranteedImageAttributes() - Method in class ChannelGenerator
-
- guaranteedImageAttributes() - Method in class ObjectsAsGrayscaleGenerator
-
- guaranteedImageAttributes() - Method in class ObjectAsMaskGenerator
-
- guaranteedImageAttributes() - Method in class ObjectsAsRGBGenerator
-
- guaranteedImageAttributes() - Method in class DrawObjectOnStackGenerator
-
- guaranteedImageAttributes() - Method in class ExtractBoundingBoxAreaFromStackGenerator
-
- guaranteedImageAttributes() - Method in class DisplayStackGenerator
-
- guaranteedImageAttributes() - Method in class FlattenStackGenerator
-
- guaranteedImageAttributes() - Method in class RasterGenerator
-
Guarantees on the attributes of all images created by the generator.
- guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToDisplayStack
-
- guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToRaster
-
- guaranteedImageAttributes() - Method in class StackGenerator
-
- guaranteedImageAttributes() - Method in class MarksAsUniqueValueGenerator
-
- guaranteedImageAttributes() - Method in class MarksGeneratorBase
-
- GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Guesses dimensions from the input-image if it exists.
- GuessDimensions() - Constructor for class GuessDimensions
-
- idAndIncrement() - Method in class MarkWithIdentifierFactory
-
- Identifiable - Interface in org.anchoranalysis.overlay.identifier
-
- IdentifiablePair<T extends Identifiable> - Class in org.anchoranalysis.mpp.pair
-
Pair of marks
- IdentifiablePair(T, T) - Constructor for class IdentifiablePair
-
- identifier(Optional<String>) - Method in class ExperimentIdentifier
-
Creates an identifier for the experiment
- identifier(Optional<String>) - Method in class ExperimentIdentifierAuto
-
- identifier(Optional<String>) - Method in class ExperimentIdentifierConstant
-
- identifier() - Method in class SingleFileInputBase
-
- identifier() - Method in interface InputFromManager
-
A unique name associated with the input.
- identifier() - Method in class InputFromManagerDelegate
-
- identifier() - Method in class MultiInput
-
- identifier() - Method in class Mark
-
- identifier() - Method in class AnnotationGroup
-
- identifier() - Method in class CoupledManifests
-
- identifier() - Method in class ManifestCouplingDefinition
-
- identifierAsPath() - Method in interface InputFromManager
-
- IdentifierByProperty - Class in org.anchoranalysis.image.core.object.properties
-
- IdentifierByProperty(String) - Constructor for class IdentifierByProperty
-
- IdentifierFromMark - Class in org.anchoranalysis.mpp.mark
-
- IdentifierFromMark() - Constructor for class IdentifierFromMark
-
- IdentifierFromOverlay - Class in org.anchoranalysis.overlay.identifier
-
- IdentifierFromOverlay() - Constructor for class IdentifierFromOverlay
-
- IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter
-
- IdentifierModulo<T> - Class in org.anchoranalysis.core.identifier.getter
-
- IdentifierModulo() - Constructor for class IdentifierModulo
-
- IdentifierModulo(IdentifierGetter<T>, int) - Constructor for class IdentifierModulo
-
- IdentifyByIteration<T> - Class in org.anchoranalysis.core.identifier.getter
-
- IdentifyByIteration() - Constructor for class IdentifyByIteration
-
- IdentifyDelegateToOverlays - Class in org.anchoranalysis.overlay.identifier
-
- IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection) - Constructor for class IdentifyDelegateToOverlays
-
- IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection, boolean) - Constructor for class IdentifyDelegateToOverlays
-
- IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a unique id number to each object.
- IdentifyObjects() - Constructor for class IdentifyObjects
-
- Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- Identity() - Constructor for class Identity
-
- IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- IdentityImposeValueRelationToHistogram() - Constructor for class IdentityImposeValueRelationToHistogram
-
- idFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes
-
ID for a particular object
- IfCondition<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional
-
The result of featureCondition is compared to a threshold, and then either the underlying feature
is calculated (positive case), or featureElse is (negative case)
- IfCondition() - Constructor for class IfCondition
-
- IfConditionWithinRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Calculates a value if a condition lies within a certain range, otherwise returns constants
- IfConditionWithinRange() - Constructor for class IfConditionWithinRange
-
- IfElse - Class in org.anchoranalysis.image.io.bean.object.draw
-
Branches to two different writers depending on a binary condition.
- IfElse(IfElse.Condition, DrawObject, DrawObject) - Constructor for class IfElse
-
- IfElse() - Constructor for class IfElse
-
- IfElse.Condition - Interface in org.anchoranalysis.image.io.bean.object.draw
-
- IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if greater than a threshold, recalculates from a
second delegate.
- IfGreaterThan() - Constructor for class IfGreaterThan
-
- IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both
masks, modifying {mask} with the result.
- IfHighLow() - Constructor for class IfHighLow
-
- IfIncrementingNumberRequested - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
Multiplexes between two
PathPrefixers depending on whether an
incrementing number
sequence was output was requested.
- IfIncrementingNumberRequested() - Constructor for class IfIncrementingNumberRequested
-
- IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
- IfKeyValueCondition() - Constructor for class IfKeyValueCondition
-
- IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if less than a threshold, recalculates from a
second delegate.
- IfLessThan() - Constructor for class IfLessThan
-
- IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is returned if it's non-empty (at least one ON voxel) otherwise maskElse is returned.
- IfNotEmpty() - Constructor for class IfNotEmpty
-
- IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is returned if the mask (treated as an object) passed an object-filter,
otherwise maskElse is returned.
- IfObjectFilter() - Constructor for class IfObjectFilter
-
- ifOptionWithoutArgument(String, Consumer<T>) - Method in class AddOptionsFromCommandLine
-
Executes consumer if an option exists without any argument.
- ifOptionWithSingleArgument(String, CheckedBiConsumer<T, String, E>) - Method in class AddOptionsFromCommandLine
-
Executes consumer if an option exists with a single argument.
- IfOutsideRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Clamps a value if it lies outside the range - instead returning particular constants if below or
above an acceptable range
- IfOutsideRange() - Constructor for class IfOutsideRange
-
- IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Multiplexes between two object-collection-providers depending on whether a parameter value equals
a particular string
- IfParamEqual() - Constructor for class IfParamEqual
-
- IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
- IfParamEquals() - Constructor for class IfParamEquals
-
- IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
Base class which multiplexes between the current mask and an alternative depending if a condition
is met.
- IfPredicateBase() - Constructor for class IfPredicateBase
-
- ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class OptionalUtilities
-
- ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class CommandLineExtracter
-
Executes a
Consumer if an option is present.
- ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class AddOptionsFromCommandLine
-
- IfRelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
Multiplexes between two namers depending on if the relative-to-directory option is
selected.
- IfRelativeToDirectory() - Constructor for class IfRelativeToDirectory
-
- IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is a particular stack exists (at least one ON voxel) otherwise maskElse is returned.
- IfStackExists() - Constructor for class IfStackExists
-
- IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Creates a new channel which is a merged version of two input channels according to rules.
- IfVoxelZero() - Constructor for class IfVoxelZero
-
- IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed unless the name's first character is an underscore.
- IgnoreUnderscorePrefix() - Constructor for class IgnoreUnderscorePrefix
-
- IgnoreUnderscorePrefixUnless - Class in org.anchoranalysis.io.output.bean.rules
-
Like
IgnoreUnderscorePrefix for all first and level-outputs unless a particular outputs
are explicitly specified.
- IgnoreUnderscorePrefixUnless(StringSet) - Constructor for class IgnoreUnderscorePrefixUnless
-
Create with first-level output names
- IgnoreUnderscorePrefixUnless() - Constructor for class IgnoreUnderscorePrefixUnless
-
- image() - Method in class MarksInitialization
-
- ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Assigns a label to each image and copies into subdirectories for each label, and creates a
labelling CSV.
- ImageAssignLabel() - Constructor for class ImageAssignLabel
-
- ImageBean<T> - Class in org.anchoranalysis.image.bean
-
- ImageBean() - Constructor for class ImageBean
-
- ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
- ImageCSVLabeller() - Constructor for class ImageCSVLabeller
-
- ImageCSVLabellerInitialization - Class in org.anchoranalysis.plugin.image.task.labeller
-
- ImageCSVLabellerInitialization(FileLabelMap<String>) - Constructor for class ImageCSVLabellerInitialization
-
- ImageFileFormat - Enum in org.anchoranalysis.core.format
-
A type of image format that are read/written to the filesystem, together with the extensions it
may use.
- ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert
-
How to shape the image (across various dimensions) after the copying
- ImageFileShape(Dimensions, int, int) - Constructor for class ImageFileShape
-
- ImageInitialization - Class in org.anchoranalysis.image.bean.nonbean.init
-
- ImageInitialization(SharedObjects) - Constructor for class ImageInitialization
-
- ImageInitialization(SharedObjects, Optional<ImageSizeSuggestion>) - Constructor for class ImageInitialization
-
- ImageInitializationFactory - Class in org.anchoranalysis.image.io
-
- ImageIOException - Exception in org.anchoranalysis.image.io
-
- ImageIOException(String) - Constructor for exception ImageIOException
-
- ImageIOException(Throwable) - Constructor for exception ImageIOException
-
- ImageIOException(String, Throwable) - Constructor for exception ImageIOException
-
- ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
- ImageIOWriter() - Constructor for class ImageIOWriter
-
- ImageJConversionException - Exception in org.anchoranalysis.io.imagej.convert
-
When conversion to ImageJ data/type is not possible, or an error occurs during conversion.
- ImageJConversionException(String) - Constructor for exception ImageJConversionException
-
Creates with a message.
- ImageJConversionException(Exception) - Constructor for exception ImageJConversionException
-
Creates with a message.
- ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Base class for writing a raster using ImageJ.
- ImageJRasterWriter() - Constructor for class ImageJRasterWriter
-
- ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image
-
A single label that pertains to an image.
- ImageLabelAnnotation(String) - Constructor for class ImageLabelAnnotation
-
- ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Associates a label with an image.
- ImageLabeller() - Constructor for class ImageLabeller
-
- ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Maps one set of labels to another
- ImageLabellerStringMap() - Constructor for class ImageLabellerStringMap
-
- ImageLabellerStringMapInitialization<T> - Class in org.anchoranalysis.plugin.image.task.labeller
-
- ImageLabellerStringMapInitialization(Map<String, String>, T) - Constructor for class ImageLabellerStringMapInitialization
-
- ImageMoments - Class in org.anchoranalysis.math.statistics.moment
-
The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of
points
- ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class ImageMoments
-
Calculates the second-moments from the covariance of a matrix of points.
- ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A base class for features that are calculated using image-moments
- ImageMomentsBase() - Constructor for class ImageMomentsBase
-
- ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
Summarizes the size of images.
- ImageSize() - Constructor for class ImageSize
-
- ImageSizeSuggestion - Interface in org.anchoranalysis.image.core.dimensions.size.suggestion
-
A suggestion on a size for an image.
- ImageSizeSuggestionFactory - Class in org.anchoranalysis.image.core.dimensions.size.suggestion
-
- ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator
-
- ImgLib2Lanczos() - Constructor for class ImgLib2Lanczos
-
- ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator
-
- ImgLib2Linear() - Constructor for class ImgLib2Linear
-
- immutableAdd(Point2i, Point2i) - Static method in class Point2i
-
Performs an addition without changing any values in an existing point
- immutableAdd(Tuple3d, Tuple3d) - Static method in class Point3d
-
Performs an addition without changing any values in an existing point
- immutableAdd(Point3d, int, int, int) - Static method in class Point3d
-
Performs an addition without changing any values in an existing point
- immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i
-
Performs an addition without changing any values in an existing point
- immutableAdd(ReadableTuple3i, int, int, int) - Static method in class Point3i
-
Performs an addition without changing any values in an existing point
- immutableScale(Tuple3d, int) - Static method in class Point3d
-
Performs a scale without changing any values in an existing point
- immutableScale(ReadableTuple3i, int) - Static method in class Point3i
-
Performs a scale without changing any values in an existing point
- immutableSubtract(Tuple3d, Tuple3d) - Static method in class Point3d
-
Performs a subtraction without changing any values in an existing point
- immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i
-
Performs a subtraction without changing any values in an existing point
- ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Imposes minima in seed locations on the input-channel before performing the segmentation
- ImposeMinima() - Constructor for class ImposeMinima
-
- imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class MinimaImposition
-
- imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class MinimaImpositionGrayscaleReconstruction
-
- imposeMinimumRadius(double) - Method in class FitResult
-
- ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Adds an explicit
Resolution to an image after it has been read.
- ImposeResolution() - Constructor for class ImposeResolution
-
- IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
- IncludeBeanFactory() - Constructor for class IncludeBeanFactory
-
- includeFirst() - Method in class MergedPairsInclude
-
- includeFirstOrSecond() - Method in class MergedPairsInclude
-
- includeGroupInExperiment(boolean) - Method in class FeatureSource
-
Iff true, group columns are added to the CSV exports, and other group exports may occur in
sub-directories.
- includeGroupInExperiment(boolean) - Method in class FromHistogram
-
- includeGroupInExperiment(boolean) - Method in class FromImage
-
- includeGroupInExperiment(boolean) - Method in class FromObjects
-
If either a group-generator is defined or there's more than one provider, then groups should
be included
- IncludeListFactory<T> - Class in org.anchoranalysis.bean.xml.factory
-
- IncludeListFactory() - Constructor for class IncludeListFactory
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaOr
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class ArbitraryPointCommon
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class BoundingBoxIntersection
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaFeatureRelationThreshold
-
- IncludeMarksFailureException - Exception in org.anchoranalysis.mpp.feature.addcriteria
-
- IncludeMarksFailureException(String) - Constructor for exception IncludeMarksFailureException
-
- IncludeMarksFailureException(Exception) - Constructor for exception IncludeMarksFailureException
-
- includeMerged() - Method in class MergedPairsInclude
-
- IncludeRandomObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
-
1.
- IncludeRandomObjects() - Constructor for class IncludeRandomObjects
-
- includeSecond() - Method in class MergedPairsInclude
-
- IncompleteElementRange - Interface in org.anchoranalysis.io.manifest.sequencetype
-
An incomplete range of discrete integers (like
BoundedRangeIncomplete but with a
string-representation for each index.
- IncorrectImageSizeException - Exception in org.anchoranalysis.image.core.dimensions
-
- IncorrectImageSizeException(String) - Constructor for exception IncorrectImageSizeException
-
- IncorrectImageSizeException(Exception) - Constructor for exception IncorrectImageSizeException
-
- IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype
-
- IncorrectVoxelTypeException(String) - Constructor for exception IncorrectVoxelTypeException
-
- IncorrectVoxelTypeException(Throwable) - Constructor for exception IncorrectVoxelTypeException
-
- incr(int) - Method in class AggIDCounter
-
- incr(Reporting<S>) - Method in class PeriodTriggerBank
-
- IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
- IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class IncreaseFeatureCondition
-
- increasingIntegers(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory
-
- IncreasingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
-
Indices must be integers that always increase as added.
- IncreasingIntegers() - Constructor for class IncreasingIntegers
-
- increment() - Method in class Counter
-
Increases the counter by one.
- increment(double) - Method in class RunningSum
-
Adds a new item to the sum, and increments the count by 1.
- increment(double, long) - Method in class RunningSum
-
Increments both the sum and count by particular values
- increment(RunningSum) - Method in class RunningSum
-
Increments (adds) an existing
RunningSum to the current.
- increment(Point2i) - Method in class RunningSumPoint
-
- increment(Point2d) - Method in class RunningSumPoint
-
- increment(Point3i) - Method in class RunningSumPoint
-
- increment(Point3d) - Method in class RunningSumPoint
-
- increment(Tuple3d) - Method in class Tuple3d
-
- incrementBy(int) - Method in class Counter
-
Increases the counter by a specific value.
- incrementCount(T) - Method in class SummarizerNamedChannels
-
- incrementCount(T) - Method in class FrequencyMap
-
- incrementCounter() - Method in class RecordingCounter
-
Increments the counter.
- incrementEnergy(double) - Method in class Aggregator
-
- incrementIndex() - Method in class KernelPointCursor
-
- incrementingByOne(String, OutputterChecked) - Method in class OutputSequenceStackFactory
-
Creates an sequence of stacks in a subdirectory with a number in the outputted file name that
increments each time by one.
- incrementingByOne(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory
-
Writes elements to directory, with an incrementing integer in the filename.
- incrementingByOneCurrentDirectory(String, String, int, OutputterChecked) - Method in class OutputSequenceStackFactory
-
Creates a sequence of stacks in the current context's directory with a number in the
outputted file name that increments each time by one.
- incrementingByOneCurrentDirectory(String, String, int) - Method in class OutputSequenceFactory
-
Writes elements to the current directory, with an incrementing integer in the filename.
- incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class OutputSequenceFactory
-
Writes file for each element in a stream with an incrementing integer sequence in the
outputted file-name.
- incrementingIntegers(OutputPatternIntegerSuffix, int, int) - Method in class OutputSequenceFactory
-
- IncrementingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
-
- IncrementingIntegers() - Constructor for class IncrementingIntegers
-
- IncrementingIntegers(int) - Constructor for class IncrementingIntegers
-
- IncrementingIntegers(int, int) - Constructor for class IncrementingIntegers
-
- IncrementingNumber - Class in org.anchoranalysis.io.output.bean.path.prefixer
-
Outputs an incrementing number for each output that occurs.
- IncrementingNumber(String) - Constructor for class IncrementingNumber
-
- IncrementingNumber() - Constructor for class IncrementingNumber
-
- incrementKernelAcceptance(int) - Method in class Aggregator
-
- incrementKernelProp(int) - Method in class Aggregator
-
- incrementSize(double) - Method in class Aggregator
-
- incrementTemperature(double) - Method in class Aggregator
-
- incrementValue(int) - Method in class Histogram
-
- incrementValueBy(int, int) - Method in class Histogram
-
- incrementValueBy(int, long) - Method in class Histogram
-
long version of incrValBy
- incrementWorker() - Method in class ProgressMultiple
-
- incrementX() - Method in class KernelPointCursor
-
- incrementX() - Method in class Point2i
-
- incrementX(int) - Method in class Point2i
-
- incrementX(double) - Method in class Tuple3d
-
- incrementX() - Method in class Tuple3i
-
- incrementX(int) - Method in class Tuple3i
-
- incrementXTwice() - Method in class KernelPointCursor
-
- incrementY() - Method in class KernelPointCursor
-
- incrementY() - Method in class Point2i
-
- incrementY(int) - Method in class Point2i
-
- incrementY(double) - Method in class Tuple3d
-
- incrementY() - Method in class Tuple3i
-
- incrementY(int) - Method in class Tuple3i
-
- incrementYTwice() - Method in class KernelPointCursor
-
- incrementZ() - Method in class KernelPointCursor
-
- incrementZ(double) - Method in class Tuple3d
-
- incrementZ() - Method in class Tuple3i
-
- incrementZ(int) - Method in class Tuple3i
-
- incrementZTwice() - Method in class KernelPointCursor
-
- IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts each channel independently and creates a single-channeled stack from the conversion.
- IndependentChannels() - Constructor for class IndependentChannels
-
- index(int) - Method in class IntegerRange
-
Maps an original integer to it's index from (0..size]
- Indexable - Class in org.anchoranalysis.core.index
-
Holds a single-index which is hashable and comparable.
- Indexable(int) - Constructor for class Indexable
-
- IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy
-
- IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class IndexableMarksWithEnergy
-
- IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
An output-name with an index somehow appended or prepended in a particular style.
- IndexableOutputNameStyle() - Constructor for class IndexableOutputNameStyle
-
- IndexableOutputNameStyle(String) - Constructor for class IndexableOutputNameStyle
-
- IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class IndexableOutputNameStyle
-
Copy constructor
- IndexableOverlays - Class in org.anchoranalysis.overlay
-
- IndexableOverlays(int, OverlayCollection) - Constructor for class IndexableOverlays
-
- IndexBridge<T> - Class in org.anchoranalysis.core.index
-
- IndexBridge(GetterFromIndex<T>) - Constructor for class IndexBridge
-
- IndexByChannel<T> - Class in org.anchoranalysis.mpp.index
-
- IndexByChannel() - Constructor for class IndexByChannel
-
- IndexByRegion<T> - Class in org.anchoranalysis.mpp.index
-
- IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class IndexByRegion
-
- indexDistanceMaxToClosestPoint(Point3i, List<ContiguousVoxelPath>, int) - Static method in class FindMinimumDistance
-
The index of whichever of the ContiguousPixelPaths has the nearest point
- IndexedCSVRows - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
Stores the rows from the CSV file.
- IndexedCSVRows(ReadByLine, ColumnDefinition) - Constructor for class IndexedCSVRows
-
Creates an index of the rows of the CSV file according to a particular columnDefinition
- IndexedRegionBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- IndexedRegionBase() - Constructor for class IndexedRegionBase
-
- IndexGettableSettable - Interface in org.anchoranalysis.core.index
-
- IndexGetter - Interface in org.anchoranalysis.core.index
-
- indexIncr(String) - Method in class SequenceMemory
-
- indexInitialPoint() - Method in class ContiguousVoxelPath
-
- indexOf(String) - Method in class FeatureNameMapToIndex
-
The index for a particular featureName
- indexOf(Mark) - Method in class VoxelizedMarksWithEnergy
-
- indexOf(Object) - Method in class UpdatableMarksList
-
- indexOf(Mark) - Method in class MarkCollection
-
- IndexRange - Class in org.anchoranalysis.core.index
-
Specifying a sub-range of indices.
- IndexRange(int, int) - Constructor for class IndexRange
-
- IndexRangeFactory - Class in org.anchoranalysis.core.index
-
- IndexSetter - Interface in org.anchoranalysis.core.index
-
- indexUniquePixel - Variable in class ColumnDefinition
-
- IndirectlyFromListBeanFactory<T extends AnchorBean<T>,S> - Class in org.anchoranalysis.bean.xml.factory
-
- IndirectlyFromListBeanFactory(CheckedFunction<List<T>, S, ? extends Exception>) - Constructor for class IndirectlyFromListBeanFactory
-
- informLatestState(T) - Method in class Kernel
-
Called every time a proposal is accepted, so a kernel can potentially keep track of the state
of the current image
- informLatestState(T) - Method in class KernelIndependent
-
- init(P, Logger) - Method in class InitializableBean
-
- init(T, Logger) - Method in interface BeanInitializer
-
- init(FeatureInitialization, Logger) - Method in interface FeatureSessionCache
-
Initializes the cache.
- init(FeatureInitialization, Feature<T>, Logger) - Method in interface InitializableFeature
-
- init(ArrangeStack, List<RGBStack>) - Method in class RasterArranger
-
- init(List<Histogram>, Optional<Dictionary>) - Method in class VoxelScore
-
Initializes the voxels-score.
- init(ChannelGetter, InputOutputContext) - Method in class ChannelFilter
-
- init(Path) - Method in class Manifest
-
- init(BeanInstanceMap) - Method in class OutputWriteSettings
-
- init() - Method in class MarksWithEnergyBreakdown
-
- init(VoxelPartitionFactory<T>, int, int, int) - Method in class IndexByChannel
-
- init(MarksInitialization, Logger) - Method in class ReportFeatureEvaluator
-
- init() - Method in class KernelProposer
-
- init(Generator<T>) - Method in class PeriodicSubdirectoryReporter
-
- init() - Method in class TerminationCondition
-
- init() - Method in class TerminationConditionListOr
-
- init() - Method in class TriggerTerminationCondition
-
- init(List<Histogram>, Optional<Dictionary>) - Method in class CalculateLevelBase
-
- init(List<Histogram>, Optional<Dictionary>) - Method in class FromDictionaryBase
-
- init(List<Histogram>, Optional<Dictionary>) - Method in class IdentityImposeValueRelationToHistogram
-
- init(List<Histogram>, Optional<Dictionary>) - Method in class NormalizeByMax
-
- init(Logger) - Method in interface AfterCondition
-
- init(Logger) - Method in class IncreaseFeatureCondition
-
- init(Path) - Method in class BinaryOutcomeImageLabeller
-
- init(Path) - Method in class ImageCSVLabeller
-
- init(Path) - Method in class ImageLabeller
-
Should be called once before calling any other methods
- init(Path) - Method in class ImageLabellerStringMap
-
- init(KernelBirth<T>, KernelDeath<T>) - Method in class KernelReplace
-
Must be called before makeProposal
- init() - Method in class NumberIterations
-
- init() - Method in class UnchangedBase
-
- init() - Method in class UnchangedScore
-
- init() - Method in class UnchangedSize
-
- initBeanInstance(Object, BeanDeclaration, Object) - Method in class AnchorDefaultBeanFactory
-
- initBeforeCalc(KernelCalculationContext) - Method in class Kernel
-
- initBeforeCalc(KernelCalculationContext) - Method in class KernelIndependent
-
- initBeforeCalc(KernelCalculationContext) - Method in class KernelProposer
-
- InitException - Exception in org.anchoranalysis.core.exception
-
An exception that occurs when initializing something, and it doesn't succeed
- InitException(String) - Constructor for exception InitException
-
- InitException(Throwable) - Constructor for exception InitException
-
- InitException(String, Throwable) - Constructor for exception InitException
-
- initHeaders(String[]) - Method in class ColumnDefinition
-
- initHeaders(String[]) - Method in class Pairwise
-
- initHeaders(String[]) - Method in class Single
-
- InitializableBean<B,P extends BeanInitialization> - Class in org.anchoranalysis.bean.initializable
-
A bean that must be initialized with some parameters before being used.
- InitializableBean(PropertyInitializer<P>, PropertyDefiner) - Constructor for class InitializableBean
-
- InitializableFeature<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate
-
A feature that should be initialized with
FeatureInitialization (or a sub-class) before
any calculations occur.
- InitializationContext - Class in org.anchoranalysis.experiment.io
-
Context for creating initialization-params.
- InitializationContext(InputOutputContext) - Constructor for class InitializationContext
-
- InitializationContext(InputOutputContext, Optional<ImageSizeSuggestion>) - Constructor for class InitializationContext
-
- InitializationFactory - Class in org.anchoranalysis.image.feature.calculator
-
- InitializationFactory - Class in org.anchoranalysis.plugin.image.task.stack
-
- InitializationWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature
-
- InitializationWithEnergyStack(EnergyStack, InitializationContext) - Constructor for class InitializationWithEnergyStack
-
- InitializationWithEnergyStack(ImageInitialization, EnergyStack) - Constructor for class InitializationWithEnergyStack
-
- initializePhase(int) - Method in class HungarianAlgorithm
-
Initialize the next phase of the algorithm by clearing the committed workers and jobs sets
and by initializing the slack arrays to the values corresponding to the specified root
worker.
- initializerForMarksBeans() - Static method in class MarksBean
-
Creates a property-initializes for MPP-Beans
- initialKernel() - Method in class KernelProposer
-
- initRecursive(P, Logger) - Method in class InitializableBean
-
Inits this object, and all children objects, so long as they have P Once a Bean doesn't have
P, the children are not evaluated
- initRecursive(Logger) - Method in class NullParamsBean
-
- initRecursive(FeatureInitialization, Logger) - Method in class FeatureList
-
- initRecursive(FeatureInitialization, Logger) - Method in class SharedFeatureSet
-
- initRecursiveWithInitializer(PropertyInitializer<?>, Logger) - Method in class InitializableBean
-
Initializes the bean and recursively all contained beans (who have compatible initialization
requirements)
- initSource(int, int) - Method in interface ProcessChangedPointAbsoluteMasked
-
The value and offset for the source point (around which we process neighbors)
- initSource(Point3i, int, int) - Method in interface ProcessVoxelNeighbor
-
Specify the source-point (of which all the processed points are neighbors)
- initSource(int, int) - Method in interface ProcessVoxelNeighborAbsolute
-
The value and offset for the source point (around which we process neighbors)
- initSource(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- initSource(int, int) - Method in class WrapAbsoluteAsMasked
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class RandomCollectionWithAddCriteria
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class EnergySavedPairs
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class UpdatableMarksList
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in interface UpdatableMarks
-
- initWithProposerSharedObjects(MarksInitialization, Logger) - Method in class KernelProposer
-
- input() - Method in class ExecutionArguments
-
Arguments to help determine the input to the experiment.
- INPUT_IMAGE - Static variable in class StackIdentifiers
-
- InputArguments - Class in org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment's input in addition to its bean
specification.
- InputArguments() - Constructor for class InputArguments
-
- InputBound<T,S> - Class in org.anchoranalysis.experiment.task
-
Input for executing a task, associated with shared-state and other parameters.
- InputBound(T, S, Manifest, boolean, InputOutputContextStateful, InputOutputContextStateful) - Constructor for class InputBound
-
- InputContextParams - Class in org.anchoranalysis.io.input
-
Additional paramaters that offer context for many beans that provide input-functions.
- InputContextParams() - Constructor for class InputContextParams
-
- InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParam<Path> factory for inputs.
- InputFromManager - Interface in org.anchoranalysis.io.input
-
One particular input for processing.
- InputFromManagerDelegate<T extends InputFromManager> - Class in org.anchoranalysis.io.input
-
A base class for
InputFromManager-implementing classes that delegate to another.
- InputFromManagerDelegate(T) - Constructor for class InputFromManagerDelegate
-
- InputManager<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean
-
Base class for describing the inputs.
- InputManager() - Constructor for class InputManager
-
- InputManagerParams - Class in org.anchoranalysis.io.input.bean
-
Parameters passed to an InputManager to generate input-objects
- InputManagerParams(InputContextParams, Progress, Logger) - Constructor for class InputManagerParams
-
- InputManagerUnary<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean
-
- InputManagerUnary() - Constructor for class InputManagerUnary
-
- InputManagerWithStackReader<T extends InputFromManager> - Class in org.anchoranalysis.image.io.bean.stack.reader
-
- InputManagerWithStackReader() - Constructor for class InputManagerWithStackReader
-
- inputName() - Method in class StackWithMap
-
- InputOutputContext - Interface in org.anchoranalysis.io.output.outputter
-
A context for performing input generally and outputting to a particular output-directory.
- InputOutputContextStateful - Class in org.anchoranalysis.experiment.task
-
- InputOutputContextStateful(ExecutionArguments, Outputter, StatefulMessageLogger, ErrorReporter) - Constructor for class InputOutputContextStateful
-
- InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter
-
- InputOutputContextSubdirectoryCache(InputOutputContext, ManifestDirectoryDescription, boolean) - Constructor for class InputOutputContextSubdirectoryCache
-
- InputOutputExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.io
-
- InputOutputExperiment() - Constructor for class InputOutputExperiment
-
- InputProcessContext<S> - Class in org.anchoranalysis.plugin.image.task.feature
-
- InputProcessContext(ExportFeatureResultsAdder, S, FeatureNameList, Optional<String>, InputOutputContext) - Constructor for class InputProcessContext
-
- InputReadFailedException - Exception in org.anchoranalysis.io.input
-
- InputReadFailedException(String) - Constructor for exception InputReadFailedException
-
- InputReadFailedException(Throwable) - Constructor for exception InputReadFailedException
-
- InputReadFailedException(String, Throwable) - Constructor for exception InputReadFailedException
-
- inputs(InputManagerParams) - Method in class AnnotationInputManager
-
- inputs(InputManagerParams) - Method in class InputManager
-
Creates a list of inputs given particular parameters.
- inputs(InputManagerParams) - Method in class InputManagerUnary
-
- inputs() - Method in class InputsWithDirectory
-
The inputs.
- inputs(InputManagerParams) - Method in class MultiInputManager
-
- inputs(InputManagerParams) - Method in class AnnotationComparisonInputManager
-
- inputs(InputManagerParams) - Method in class GroupFiles
-
- inputs(InputManagerParams) - Method in class NamedChannels
-
- inputs(InputManagerParams) - Method in class NamedChannelsAppend
-
- inputs(InputManagerParams) - Method in class Concatenate
-
- inputs(InputManagerParams) - Method in class NamedFiles
-
- inputs(InputManagerParams) - Method in class NamedFilesWithDirectory
-
- inputs(InputManagerParams) - Method in class CoupledManifestsInputManager
-
- inputs(InputManagerParams) - Method in class ConvertNamedChannelsToStack
-
- inputs(InputManagerParams) - Method in class Stacks
-
- inputs(ImageInitialization, Logger) - Method in class ExportObjectsBase
-
- inputs(InputManagerParams) - Method in class FromCSVInputManager
-
- inputs(InputManagerParams) - Method in class MultiInputManagerQuick
-
- inputs(InputManagerParams) - Method in class NamedChannelsQuick
-
- inputSelectParam(CommandLine) - Static method in class SelectParamFactory
-
Can point to either:
a path ending in .xml, assumed to BeanXML for an input manager
a directory, set as an the inputDirectory in the input-context
a string with a wild-card, assumed to be a glob, set into the input-context as a glob
a string with a period and without any forward or backwards slashes, set into the
input-context as an extension to match
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class InputManagerUnary
-
Calculates the inputs to return given the inputs from the delegate.
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class BranchIfDebug
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class Exclude
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class FilterCsvColumn
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class FilterDescriptiveName
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class FilterIfDebug
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class Limit
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class Shuffle
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class ShuffleIfRequested
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParams) - Method in class SortAlphabetically
-
- InputsWithDirectory<T extends InputFromManager> - Class in org.anchoranalysis.io.input
-
All inputs for an experiment, together with any parent directory which is specified as a parent
for these inputs.
- InputsWithDirectory(List<T>) - Constructor for class InputsWithDirectory
-
Creates without any parent directory.
- InputsWithDirectory(List<T>, Optional<Path>) - Constructor for class InputsWithDirectory
-
- inputType() - Method in class Feature
-
The class corresponding to feature input-type (i.e.
- inputType() - Method in class FeatureDoubleElem
-
- inputType() - Method in class FeatureListElem
-
- inputType() - Method in class FeatureOperator
-
- inputType() - Method in class FeatureUnary
-
- inputType() - Method in class FeatureResults
-
- inputType() - Method in class FeatureEnergy
-
- inputType() - Method in class FeatureHistogram
-
- inputType() - Method in class FeatureStack
-
- inputType() - Method in class FeatureObjectCollection
-
- inputType() - Method in class FeaturePairObjects
-
- inputType() - Method in class FeatureSingleObject
-
- inputType() - Method in class AsSingle
-
- inputType() - Method in class FeatureAllMemo
-
- inputType() - Method in class FeaturePairMemo
-
- inputType() - Method in class FeatureSingleMemo
-
- inputType() - Method in class FeatureMarkCollection
-
- inputType() - Method in class FeatureMark
-
- inputType() - Method in class FeatureSingleObjectFromShared
-
- inputType() - Method in class AsMark
-
- inputType() - Method in class AsObject
-
- inputTypesExpected() - Method in class Task
-
Highest class(es) that will function as a valid input.
- InputTypesExpected - Class in org.anchoranalysis.experiment.task
-
A list of base (parent) classes for input-types that a task expects
- InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class InputTypesExpected
-
- inputTypesExpected() - Method in class HelloWorld
-
- inputTypesExpected() - Method in class AggregateAnnotations
-
- inputTypesExpected() - Method in class CompareAnnotations
-
- inputTypesExpected() - Method in class ExportFeatures
-
- inputTypesExpected() - Method in class FeatureSource
-
Highest class(es) that will function as a valid input.
- inputTypesExpected() - Method in class FromHistogram
-
- inputTypesExpected() - Method in class FromImage
-
- inputTypesExpected() - Method in class GroupedStackBase
-
- inputTypesExpected() - Method in class ImageAssignLabel
-
- inputTypesExpected() - Method in class RasterTask
-
- inputTypesExpected() - Method in class ScaleImage
-
- inputTypesExpected() - Method in class SegmentInstanceWithModel
-
- inputTypesExpected() - Method in class ExtractSlice
-
- inputTypesExpected() - Method in class CombineCSV
-
- inputTypesExpected() - Method in class CopyFiles
-
- inputTypesExpected() - Method in class SummarizeInputs
-
- inputTypesExpected() - Method in class ConvertNamedChannels
-
- inputTypesExpected() - Method in class Develop
-
- inputTypesExpected() - Method in class ExportReportFeaturesFromManifest
-
- inputTypesExpected() - Method in class ExportReportFeaturesFromMulti
-
- inputTypesExpected() - Method in class FromObjects
-
- inputTypesExpected() - Method in class ExportObjectsAsCroppedImages
-
- inputTypesExpected() - Method in class ExportObjectsFromCSV
-
- inputTypesExpected() - Method in class SegmentMarksFromImage
-
- insertAfter(List<Point3i>) - Method in class ContiguousVoxelPath
-
Inserts points at end of existing path.
- insertBefore(List<Point3i>) - Method in class ContiguousVoxelPath
-
Inserts points before existing path.
- insertBeginning(String) - Method in class FeatureNameList
-
Inserts a new feature-name at the beginning of the list
- insertBeginning(String[]) - Method in class FeatureNameList
-
Inserts new feature-names at the beginning of the list
- InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates an out string where $digit$ is replaced with the #digit group from a regex
- InsertRegExGroups() - Constructor for class InsertRegExGroups
-
- InsertRegExGroups(RegEx, String) - Constructor for class InsertRegExGroups
-
- InsideBoxOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
-
Creates a binary img-channel where all pixels are 'on' within a certain x, y, z coordinate range
- InsideBoxOn() - Constructor for class InsideBoxOn
-
- instance() - Static method in class NullInitialization
-
- INSTANCE - Static variable in class NoSharedState
-
- instance() - Static method in class FeatureInputNull
-
- instance() - Static method in class DefaultChildCacheFinder
-
- instance() - Static method in class ChannelFactory
-
Singleton
- INSTANCE - Static variable in class FloatVoxelType
-
- INSTANCE - Static variable in class SignedShortVoxelType
-
- INSTANCE - Static variable in class UnsignedByteVoxelType
-
- INSTANCE - Static variable in class UnsignedIntVoxelType
-
- INSTANCE - Static variable in class UnsignedShortVoxelType
-
- instance() - Static method in class VoxelsFactory
-
Singleton
- instance() - Static method in class ConfigureBioformatsLogging
-
- INSTANCE - Static variable in class All
-
A singleton instance of
All.
- INSTANCE - Static variable in class IgnoreUnderscorePrefix
-
- INSTANCE - Static variable in class None
-
A singleton instance of
None.
- INSTANCE - Static variable in class Permissive
-
- instance() - Static method in class RegionMapSingleton
-
- instance() - Static method in class ErrorNodeNull
-
- instance() - Static method in class RootPathMap
-
- InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter
-
- InsufficientPointsException() - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(String, Throwable) - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(String) - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(Throwable) - Constructor for exception InsufficientPointsException
-
- IntBinaryOperation - Interface in org.anchoranalysis.core.functional.checked
-
A binary operation on two int-values that produces an int
- IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
-
- IntegerRange(int) - Constructor for class IntegerRange
-
- IntegerRange(int, int) - Constructor for class IntegerRange
-
- IntegerSequenceContaner - Class in org.anchoranalysis.core.index.bounded
-
- IntegerSequenceContaner(int) - Constructor for class IntegerSequenceContaner
-
- integerSet() - Method in class OverlayCollection
-
- IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
Outputs a file-name involving an integer of length numberDigits with leading zeros.
- IntegerSuffixOutputNameStyle() - Constructor for class IntegerSuffixOutputNameStyle
-
- IntegerSuffixOutputNameStyle(String, int) - Constructor for class IntegerSuffixOutputNameStyle
-
- IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class IntegerSuffixOutputNameStyle
-
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Calculates a statistic from the intensity values covered by a single object-mask in a channel.
- Intensity() - Constructor for class Intensity
-
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
The intensity of a particular channel of the stack, by default the mean-intensity.
- Intensity() - Constructor for class Intensity
-
- Intensity - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- Intensity() - Constructor for class Intensity
-
- IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
- IntensityGradientBase() - Constructor for class IntensityGradientBase
-
- IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only keep objects where at least one voxel (on a particular channel) has intensity greater or
equal to a threshold.
- IntensityGreaterEqualThan() - Constructor for class IntensityGreaterEqualThan
-
- intensityMax(Voxels<T>) - Static method in class IterateVoxelsAll
-
Finds the maximum intensity-value (as an int) among all voxels.
- IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity
-
- IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
- IntensityMeanMaxSlice() - Constructor for class IntensityMeanMaxSlice
-
- IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShell() - Constructor for class IntensityMeanShell
-
- IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a shell around an object-mask using a standard dilation and erosion process
- IntensityMeanShellBase() - Constructor for class IntensityMeanShellBase
-
- IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShellMaxSlice() - Constructor for class IntensityMeanShellMaxSlice
-
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in interface Interpolator
-
Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit
buffers.
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
-
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorNone
-
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in interface Interpolator
-
Interpolates from voxelsSource to voxelsDestination for float buffers.
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
-
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorNone
-
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in interface Interpolator
-
Interpolates from voxelsSource to voxelsDestination for unsigned 16-bit
buffers.
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
-
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorNone
-
- InterpolateUtilities - Class in org.anchoranalysis.image.voxel.interpolator
-
- Interpolator - Interface in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorBean - Class in org.anchoranalysis.image.bean.interpolator
-
- InterpolatorBean() - Constructor for class InterpolatorBean
-
- InterpolatorBeanImageJ - Class in org.anchoranalysis.plugin.imagej.bean.interpolator
-
- InterpolatorBeanImageJ() - Constructor for class InterpolatorBeanImageJ
-
- InterpolatorFactory - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorImgLib2 - Class in org.anchoranalysis.image.voxel.interpolator
-
Performs interpolation using ImgLib2
- InterpolatorImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Constructor for class InterpolatorImgLib2
-
- InterpolatorImgLib2Lanczos - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorImgLib2Lanczos() - Constructor for class InterpolatorImgLib2Lanczos
-
- InterpolatorImgLib2Linear - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorImgLib2Linear() - Constructor for class InterpolatorImgLib2Linear
-
- InterpolatorImgLib2NearestNeighbor - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorImgLib2NearestNeighbor() - Constructor for class InterpolatorImgLib2NearestNeighbor
-
- InterpolatorNone - Class in org.anchoranalysis.image.voxel.interpolator
-
Doesn't do any interpolation, just copies values
- InterpolatorNone() - Constructor for class InterpolatorNone
-
- intersect(ObjectMask, Extent) - Method in class ObjectMask
-
Intersects this object-mask with another
- IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects
-
- IntersectingObjects<T> - Class in org.anchoranalysis.image.voxel.object
-
A data-structure to efficiently determine which object-masks intersect in a collection.
- IntersectingObjects(Collection<T>, Function<T, ObjectMask>) - Constructor for class IntersectingObjects
-
Creates an r-tree for particular objects.
- Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match
-
- Intersection() - Constructor for class Intersection
-
- Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair
-
Finds the intersection of two objects and calculates a feature on it
- Intersection() - Constructor for class Intersection
-
- intersection() - Method in class BoundingBox
-
For evaluating the intersection between this bounding-box and others
- IntersectionOverUnion - Class in org.anchoranalysis.plugin.image.box
-
Calculates the intersection-over-union score a pair of bounding-boxes.
- intersectsWith(ObjectMask) - Method in class IntersectingObjects
-
All elements that intersect with a particular object.
- intersectsWith(BoundingBox) - Method in class IntersectingObjects
-
All elements that intersect with a particular bounding box.
- IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Keeps objects which intersects with ANY ONE of a collection of other objects.
- IntersectsWith() - Constructor for class IntersectsWith
-
- intersectsWith(BoundingBox) - Method in class RTree
-
Which bounding-boxes intersect with another specific bounding box?
- IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Returns only the objects that intersect with at least one object in the container
- IntersectsWithContainer() - Constructor for class IntersectsWithContainer
-
- intersectsWithStream(ObjectMask) - Method in class IntersectingObjects
-
- intersectsWithStream(BoundingBox) - Method in class RTree
-
- intersectWith(Extent) - Method in class Extent
-
Intersects this extent with another (i.e.
- intFromDoubleCeil(Point3d) - Static method in class PointConverter
-
- intFromDoubleFloor(Point2d) - Static method in class PointConverter
-
- intFromDoubleFloor(Point3d) - Static method in class PointConverter
-
- intFromFloat(Point3f, boolean) - Static method in class PointConverter
-
- INVALID_AXIS_INDEX - Static variable in class AxisTypeConverter
-
- INVALID_AXIS_STRING - Static variable in class AxisTypeConverter
-
- invalidate() - Method in interface FeatureSessionCache
-
Invalidates existing caches so all calculations occur freshly
- invalidate() - Method in interface ResettableCalculation
-
Resets the cached-calculation, so the next call to doOperationWithParams() is guaranteed to
calculation the operation, and store the value in the cache.
- invalidate() - Method in class FeatureCalculation
-
- invalidate() - Method in class FeatureCalculationMap
-
Invalidates the cache, removing any items already stored.
- invalidateExcept(Set<ChildCacheName>) - Method in interface FeatureSessionCache
-
Invalidates existing caches so all calculations occur freshly - except some particular
child-caches who are not invalidated
- InvalidPathArgumentException - Exception in org.anchoranalysis.launcher.executor.selectparam.path.convert
-
An exception throw if an invalid-path is inputted as an argument.
- InvalidPathArgumentException(String) - Constructor for exception InvalidPathArgumentException
-
- InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception InvalidPathArgumentException
-
- invert(Mask) - Static method in class MaskInverter
-
Modifies a mask so that OFF voxels become ON voxels and vice versa
- invert() - Method in class BinaryVoxels
-
Changes the OFF state to be the ON state and vice-versa.
- invert() - Method in class BinaryValuesByte
-
- invert() - Method in class ObjectMask
-
Produces a new object-mask that uses the same voxel-buffer but inverts the OFF and ON
- Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtracts each voxel from the maximum value for the channel's data type (e.g.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Switches on voxels to off and vice-versa.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.scale
-
Invert the
ScaleFactor calculated by the
scaleCalculator delegate.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a segmentation and inverts and ON and OFF bytes
- Invert() - Constructor for class Invert
-
- invert() - Method in class ScaleFactor
-
Build a new scale factor where each dimension is set to the reciprocal of its current value.
- InvertedMax<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
- InvertedMax() - Constructor for class InvertedMax
-
- invertObjectDuplicate(ObjectMask) - Static method in class MaskInverter
-
Creates a new object-mask where OFF voxels become ON voxels and vice versa
- isAcceptDirectoryErrors() - Method in class SearchDirectory
-
if true, continues when a directory-access-error occurs (logging it), otherwise throws an
exception
- isAccepted() - Method in class DualMarksAnnotation
-
- isAccepted() - Method in class KernelDescision
-
- isAccepted() - Method in class Reporting
-
- isAcceptMissingResolution() - Method in class WithResolutionBase
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- isAcceptMissingResolution() - Method in class VoxelPhysicalSize
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- isAcceptNoResolution() - Method in class ReadVoxelExtentXml
-
If false, an exception is thrown if the resolution file is missing for a particular image.
- isAcceptOutsideScene() - Method in class CheckMarkWithMask
-
- isAddName() - Method in class CombineCSV
-
- isAddOne() - Method in class Quantile
-
- isAlways2D() - Method in class StackWriteAttributes
-
True the output is guaranteed to only ever 2D i.e.
- isApplyResolution() - Method in class DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- isApplyToPath() - Method in class MatchRegularExpression
-
If true, the filter is applied to the path as a whole, not just the filename (using forward
slashes as directory separators)
- isAsPercentage() - Method in class Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal
- isAtLeastOnePositive() - Method in class MorphologicalIterations
-
Checks that at least one of iterationsDilation and iterationsErosion is more
than 0
- isAvoidBulletOnFirst() - Method in class SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- isAvoidDivideByZero() - Method in class Divide
-
- isAvoidOverlappingObjects() - Method in class PairNeighbors
-
If true, no overlapping objects are treated as pairs
- isBest() - Method in class Reporting
-
- isBest() - Method in class VoxelizedMarksChangeReporter
-
- isBigNeighborhood() - Method in class EdgeAdderParameters
-
iff true uses a big-neighborhood (8 or 26 connectivity) for dilation
- isBigNeighborhood() - Method in class Dilate
-
- isBigNeighborhood() - Method in class ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- isBigNeighborhood() - Method in class DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- isBigNeighborhood() - Method in class Dilate
-
- isBigNeighborhood() - Method in class TraverseOutlineOnImage
-
- isBinary() - Method in class StackWriteAttributes
-
Whether all channels represent a binary image.
- isBinary() - Method in class ScaleImage
-
Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling
ensures only two binary-values are ouputted.
- isBit0() - Method in class RegionMembership
-
- isBit1() - Method in class RegionMembership
-
- isBit2() - Method in class RegionMembership
-
- isBit3() - Method in class RegionMembership
-
- isBit4() - Method in class RegionMembership
-
- isBit5() - Method in class RegionMembership
-
- isBit6() - Method in class RegionMembership
-
- isBit7() - Method in class RegionMembership
-
- isBold() - Method in class TextStyle
-
Whether to bold the drawn text
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderBase
-
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderXY
-
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderZ
-
- isBufferOff(UnsignedByteBuffer) - Method in class KernelPointCursor
-
- isBufferOn(UnsignedByteBuffer) - Method in class KernelPointCursor
-
- isBySlices() - Method in class ConnectedComponentsFromMask
-
- isCalledRegisterAllPackage() - Static method in class RegisterBeanFactories
-
- isCaseSensitive() - Method in class PatternSpan
-
Iff true, a case sensitive search is used to match patterns.
- isCellUsed(int, int) - Method in class TableItemArrangement
-
- isChangeExisting() - Method in class ConvertBase
-
If true, the existing channel can be changed.
- isClearOutsideMask() - Method in class ThresholdAgainstChannel
-
- isClosed() - Method in class Contour
-
- isCollapseFilename() - Method in class FilePathAppendBase
-
- isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class FeatureInputType
-
Can these parameters be used with a particular feature?
- isCompatibleWith(Mark) - Method in interface CompatibleWithMark
-
- isCompatibleWith(Mark) - Method in class AndList
-
- isCompatibleWith(Mark) - Method in class CheckMarkWithMask
-
- isCompatibleWith(Mark) - Method in class FeatureValueCheckMark
-
- isCompatibleWith(Mark) - Method in class Not
-
- isCompatibleWith(Mark) - Method in class RadiiMinRatio
-
- isCompatibleWith(Mark) - Method in class VolumeMin
-
- isCompatibleWith(Mark) - Method in class CreateNew
-
- isCompatibleWith(Mark) - Method in class FromMarkProposer
-
- isCompatibleWith(Mark) - Method in class FromObjects
-
- isCompatibleWith(Mark) - Method in class FromProvider
-
- isCompatibleWith(Mark) - Method in class FromSerializedMarks
-
- isCompatibleWith(Mark) - Method in class Check
-
- isCompatibleWith(Mark) - Method in class Check
-
- isCompatibleWith(Mark) - Method in class MarkFromCollectionProposerUnary
-
- isCompatibleWith(Mark) - Method in class UniformRandom
-
- isCompatibleWith(Mark) - Method in class FromSerializedObject
-
- isCompatibleWith(Mark) - Method in class MarkProposerFromList
-
- isCompatibleWith(Mark) - Method in class MarkProposerReference
-
- isCompatibleWith(Mark) - Method in class MarkProposerUnary
-
- isCompatibleWith(Mark) - Method in class ObjectAsPoints
-
- isCompatibleWith(Mark) - Method in class OrientationAndRadiiProposer
-
- isCompatibleWith(Mark) - Method in class Position
-
- isCompatibleWith(Mark) - Method in class MarkMergeProposerReference
-
- isCompatibleWith(Mark) - Method in class MergeMarkEllipse
-
- isCompatibleWith(Mark) - Method in class AngleRotation
-
- isCompatibleWith(Mark) - Method in class RandomOrientation
-
- isCompatibleWith(Mark) - Method in class RandomXY
-
- isCompatibleWith(Mark) - Method in class IncludeRandomObjects
-
- isCompatibleWith(Mark) - Method in class XYOrientationExtendToZ
-
- isCompatibleWith(Mark) - Method in class RadiiProposerRepeat
-
- isCompatibleWith(Mark) - Method in class UniformRandomRadiiProposer
-
- isCompatibleWith(Mark) - Method in class MarkEllipseSimple
-
- isCompatibleWith(Mark) - Method in class MarkSplitProposerReference
-
- isCompatibleWith(Mark) - Method in class KernelBirthPartition
-
- isCompatibleWith(Mark) - Method in class KernelReplacePartition
-
- isCompatibleWith(Mark) - Method in class KernelBirthAndKill
-
- isCompatibleWith(Mark) - Method in class KernelDeath
-
- isCompatibleWith(Mark) - Method in class KernelExchange
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksFromPartition
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksProposed
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksVoxelized
-
- isCompatibleWith(Mark) - Method in class KernelMerge
-
- isCompatibleWith(Mark) - Method in class KernelSplit
-
- isCompatibleWith(Mark) - Method in class KernelBirthPixelized
-
- isCompatibleWith(Mark) - Method in class ConstantWeight
-
- isCompatibleWith(Mark) - Method in class NumberPoints
-
- isCompatibleWith(Mark) - Method in class FitPoints
-
- isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipseFitter
-
- isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipsoidFitter
-
- isCompatibleWith(Mark) - Method in class Reference
-
- isCompatibleWith(Mark) - Method in class ReflectInAxesWithinDistance
-
- isCompleted() - Method in class JobState
-
- isCompletedFailure() - Method in class JobState
-
- isCompletedSuccessfully() - Method in class JobState
-
- isConditionTrue() - Method in class DictionaryCondition
-
- isConnectedComponentID(int) - Method in class EncodedIntBuffer
-
- isConnectedComponentIDCode(int) - Method in class EncodedVoxels
-
- isConnectedComponentIDCode(int) - Method in class WatershedEncoding
-
- isConsiderForMerge() - Method in class PrioritisedVertex
-
- isConvexHull() - Method in class FitPointsFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- isCopyNonInputs() - Method in class InputArguments
-
If True, any files in the input directory that are unused as inputs, are copied to the output
directory.
- isCov() - Method in class ObjectRadiusStandardDeviation
-
- isCreateShort() - Method in class ArrangeRaster
-
- isCreateShort() - Method in class GenerateString
-
- isCreateShort() - Method in class TileWithLabels
-
- isCreateShort() - Method in class DistanceTransform3D
-
- isCreateShort() - Method in class DistanceTransformForEachObject3D
-
- isCreateShort() - Method in class CreateNew
-
If True creates an unsigned short-image
- isCsvIgnoreZeros() - Method in class ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- isDatasetNameSubdirectory() - Method in class ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- isDay() - Method in class ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output
- isDebug() - Method in class RootPath
-
If true this root is preferred, when executing a job in debugging mode
- isDebug() - Method in class ThresholdedFeature
-
- isDebugEnabled() - Method in class InputOutputContextStateful
-
- isDebugEnabled() - Method in interface InputOutputContext
-
Is debug-mode enabled?
- isDebugEnabled() - Method in class OptimizationContext
-
- isDebugMode() - Method in class PathPrefixerContext
-
Whether debug-mode is activated.
- isDebugModeActivated() - Method in class InputManagerParams
-
- isDebugModeEnabled() - Method in class ExecutionArguments
-
- isDefault() - Method in interface SelectParam
-
Is this the default option that occurs without any additional user effort?
- isDefault() - Method in class UseDefaultManager
-
- isDetailedLogging() - Method in class InputBound
-
- isDetailedLogging() - Method in class ParametersExperiment
-
Iff true, additional log messages are written to describe each job in terms of its unique
name, output folder, average execution time etc.
- isDifferentColorsForMatches() - Method in class ColorPool
-
- isDirect() - Method in class UnsignedBuffer
-
Is this buffer direct or non-direct?
- isDirect() - Method in class VoxelBuffer
-
Is this buffer direct or non-direct?
- isDirect() - Method in class VoxelBufferUnsigned
-
- isDirectionChainCode(int) - Method in class EncodedVoxels
-
- isDirectionChainCode(int) - Method in class WatershedEncoding
-
- isDisableDebugMode() - Method in class RootedFilePath
-
- isDisableDebugMode() - Method in class Rooted
-
- isDisablePathModification() - Method in class MarkAnnotationWriter
-
- isDo3D() - Method in class AnisotropicDiffusion
-
- isDo3D() - Method in class ObjectCollectionProviderMorphological
-
- isDo3D() - Method in class MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- isDo3D() - Method in class PairNeighbors
-
- isDo3D() - Method in class TouchingVoxels
-
- isDo3D() - Method in class Erode
-
- isDo3D() - Method in class NumberRemovedVoxelsAfterClosing
-
- isDo3D() - Method in class OutlineKernelBase
-
- isDo3D() - Method in class UniformRandomRadiiProposer
-
- isDrawReverseLine() - Method in class Orientation
-
- isDuplicate() - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data
This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isDuplicate() - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting
data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isEmpty() - Method in interface StringBeanCollection
-
- isEmpty() - Method in class StringList
-
- isEmpty() - Method in class StringSet
-
- isEmpty() - Method in interface NamedProvider
-
Are there any items in the provider
- isEmpty() - Method in class FeatureList
-
- isEmpty() - Method in class ResultsVectorList
-
- isEmpty() - Method in class SeedCollection
-
- isEmpty() - Method in class TimeSequence
-
- isEmpty() - Method in class ObjectCollection
-
- isEmpty() - Method in class InputsWithDirectory
-
- isEmpty() - Method in class RecordedOutputs
-
If no output-names exist.
- isEmpty() - Method in class Histogram
-
- isEmpty() - Method in class UpdatableMarksList
-
- isEmpty() - Method in class MarkCollection
-
- isEmpty() - Method in class SegmentedObjects
-
Whether no segmented objects exist.
- isEmpty() - Method in class PointRange
-
Has a valid min and max defined? In other words, has at least one point been added?
- isEmpty() - Method in class Extent
-
- isEnabled() - Method in class TextFileOutput
-
- isErodeAtBoundary() - Method in class ConvexHullBase
-
- isErrorDisconnectedObjects() - Method in class RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- isEvaluated() - Method in class CachedSupplierBase
-
- isExceptionIfEmpty() - Method in class FeatureHistogramStatistic
-
If true, then an exception is thrown if the histogram is empty, otherwise
is returned.
- isExcludeZero() - Method in class Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- isExcludeZero() - Method in class IntensityMeanMaxSlice
-
- isExcludeZero() - Method in class Intensity
-
If true, zeros are excluded from considering in the histogram
- isExecuting() - Method in class JobState
-
- isExitBeforeOptimization() - Method in class SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- isExitWithMinima() - Method in class WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- isExpandLabelZ() - Method in class TileWithLabels
-
- isExtendInZ() - Method in class ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
- isFieldAnnotatedAsOptional(Field) - Static method in class FieldAccessor
-
- isFindMaxima() - Method in class ExtractSlice
-
If true, the maxima of the score is searched for.
- isFinished() - Method in class DualMarksAnnotation
-
- isFirst() - Method in class AsSingle
-
Iff true, first object is used, otherwise the second
- isFirstDefined() - Method in class OutputEnableRulesSpecify
-
- isFirstLineHeaders() - Method in class CombineCSV
-
- isFixRandomSeed() - Method in class SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- isFlatten() - Method in class Outline
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make
it 2D
- isFlatten() - Method in class ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity
projection), so that a 2D image is produced
- isForceChangeBytes() - Method in class Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer
to reflect the existing binary-values.
- isForceDetailedLogging() - Method in class OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- isForceEagerEvaluation() - Method in class NamedChannelsAppend
-
- isForceRGB() - Method in class ArrangeRaster
-
If set, ensures every stack is converted into 3 channels
- isForwardDirectionOnly() - Method in class XYOrientationExtendToZ
-
- isGaussian() - Method in class AddEdgeFilters
-
If true, the Gaussian filter is included
- isGPU() - Method in class WithPriority
-
- isHighestTwoRadiiOnly() - Method in class RadiiRatio
-
- isIgnoreAtThreshold() - Method in class OutlineKernelBase
-
- isIgnoreCase() - Method in class FilePathPattern
-
if true, case is ignored in the pattern matching.
- isIgnoreFileNotFoundAppend() - Method in class NamedChannelsAppend
-
- isIgnoreFittingFailure() - Method in class FitPointsFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply
not included (with only a log error) If false, an exception is thrown
- isIgnoreHidden() - Method in class SearchDirectory
-
if true, case is ignored in the pattern matching.
- isIgnoreHidden() - Method in class FilePathPattern
-
Iff true, any hidden-path is not considered, and simply ignored
- isIgnoreHigherSide() - Method in class GaussianCumulative
-
- isIgnoreLowerSide() - Method in class GaussianCumulative
-
- isIgnoreMissingChannel() - Method in class IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- isIgnoreNaN() - Method in class Sum
-
If true, we ignore any NaN values.
- isIgnoreNoObjects() - Method in class SegmentInstanceWithModel
-
If true, then the outputs (outline, mask, image etc.) are not written for images that produce
no objects.
- isIgnoreOutside() - Method in class KernelApplicationParameters
-
- isIgnoreOutside() - Method in enum OutsideKernelPolicy
-
When true, any parts of the neigborhood that lie outside the scene are not considered in
kernel neighborhoods.
- isIgnoreRangeAxisOutside() - Method in class LinePlot
-
- isIgnoreZero() - Method in class RatioNonMode
-
- isIgnoreZeros() - Method in class HistogramCSVGenerator
-
Iff true bins in the histogram with a zero count are not written
- isIgnoreZIfNaN() - Method in class DistanceTransform3D
-
If the z-resolution is undefined, the z dimenion is ignored.
- isIncludeDirectories() - Method in class DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- isIncludeFeatureNames() - Method in class EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the
actual features
- isIncludeFileName() - Method in class AppendDictionary
-
- isIncludeFirst() - Method in class PairNeighbors
-
Include features for the First-object of the pair
- isIncludeMerged() - Method in class PairNeighbors
-
Include features for the Merged-object of the pair
- isIncludeSecond() - Method in class PairNeighbors
-
Include features for the Second-object of the pair
- isIncludeShell() - Method in class MaxOverlapRatio
-
- isIncludeZ() - Method in class Outline
-
If true the outline is also applied in the z-dimension, otherwise this is ignored as possible
boundary
- isIncludeZ() - Method in class NotTouchingSceneBorder
-
- isInitialized() - Method in class InitializableBean
-
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class JobProcessor
-
Is an input-object compatible with this particular task?
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class Task
-
Is an input-object compatible with this particular task?
- isInteger() - Method in class FloatVoxelType
-
- isInteger() - Method in class SignedVoxelType
-
- isInteger() - Method in class UnsignedVoxelType
-
- isInteger() - Method in class VoxelDataType
-
- isInterpolate() - Method in class AtScale
-
- isInverse() - Method in class IntersectsWithContainer
-
- isInverse() - Method in class IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is
removed)
- isInverseMask() - Method in class IntensityMeanShellBase
-
- isInvert() - Method in class MaskComparer
-
- isInvert() - Method in class FromObjects
-
- isInvert() - Method in class FilterWithRegularExpression
-
Iff true, then a file is rejected if the regular-expression matches and vice-versa.
- isInvertDecisionValue() - Method in class FeatureListProviderSVMClassifier
-
- isItemIncluded(T) - Method in class Plot
-
Whether to include this particular item in the plot?
- isKeepEntireImage() - Method in class ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
- isKeepExtremes() - Method in class Identity
-
- isKeepZ() - Method in class ImposeResolution
-
Keep the z-resolution if it is already defined
- isKeyRequired() - Method in class RegularExpression
-
- isLabel() - Method in class MontageSlices
-
If true a label is added beside every image showing the slice index
- isLeaf() - Method in class ErrorNodeImpl
-
- isLocalized() - Method in class FilesProviderWithDirectoryString
-
- isLogPath() - Method in class Rooted
-
if true, the pathIn and pathOut are logged.
- isMarksSpan(MarkCollection) - Method in class RandomCollectionWithAddCriteria
-
- isMarksSpan() - Method in class VoxelizedMarksWithEnergy
-
- isMarksSpan(MarkCollection) - Method in class EnergySavedPairs
-
- isMax() - Method in class IdentityImposeValueRelationToHistogram
-
- isMedian() - Method in class AddEdgeFilters
-
If true, the median filter is included
- isMemberFlag(byte, byte) - Method in class RegionMembership
-
- isMemberFlag(byte, byte) - Method in class RegionMembershipAnd
-
- isMemberFlag(byte, byte) - Method in class RegionMembershipOr
-
- isMemberFlag(byte) - Method in class RegionMembershipWithFlags
-
- isMemberFlagAnd(byte, byte) - Static method in class RegionMembershipUtilities
-
- isMemberFlagOr(byte, byte) - Static method in class RegionMembershipUtilities
-
- isMerge() - Method in class CutBelowThreshold
-
- isMinima(int) - Method in class EncodedIntBuffer
-
- isMinima(int) - Method in class EncodedVoxels
-
- isMip() - Method in class NumberVoxels
-
- isMip() - Method in class SurfaceNumberVoxelsBase
-
- isMip() - Method in class OverlapMIPBase
-
- isNewValuesPossible() - Method in interface Interpolator
-
Returns true if it's possible for values to be created after interpolation that aren't found
in the input-image.
- isNewValuesPossible() - Method in class InterpolatorImgLib2Lanczos
-
- isNewValuesPossible() - Method in class InterpolatorImgLib2Linear
-
- isNewValuesPossible() - Method in class InterpolatorImgLib2NearestNeighbor
-
- isNewValuesPossible() - Method in class InterpolatorNone
-
- isNoBlack() - Method in class ThresholderAutoIJ
-
- isNormalize() - Method in class Identity
-
- isNormalize() - Method in class BoundingBoxZOverlapRatio
-
- isNormalizeFeatures() - Method in class FeatureListProviderSVMClassifier
-
Normalize features
- isNoScale() - Method in class ScaleFactor
-
Does the scale-factor involve no scaling at all?
- isNumeric() - Method in class TypedValue
-
- isNumeric() - Method in class ReportFeature
-
- isNumeric() - Method in class ReportFeatureOnMark
-
- isNumeric() - Method in class ReportFeatureOnMarks
-
- isNumeric() - Method in class ReportFeatureOnObjectsBase
-
- isNumeric() - Method in class ReportFeatureWrapError
-
- isNumeric() - Method in class NumberMarksFromManifest
-
- isNumeric() - Method in class ReportFeatureForManifestFileBase
-
- isNumeric() - Method in class RootFilePathRegEx
-
- isOff(int, int, int) - Method in interface BinaryOnOffSetter
-
- isOff(Point3i) - Method in interface BinaryOnOffSetter
-
- isOff(byte) - Method in class BinaryValuesByte
-
- isOmitExperimentIdentifier() - Method in class OutputArguments
-
- isOmitExperimentIdentifier() - Method in class OutputPrefixerSettings
-
Requests that the experiment-identifier (name and index) is not included in the
output-directory path.
- isOn(int, int, int) - Method in interface BinaryOnOffSetter
-
- isOn(Point3i) - Method in interface BinaryOnOffSetter
-
- isOn(byte) - Method in class BinaryValuesByte
-
- isOn() - Method in interface OutputSequence
-
- isOn() - Method in class OutputSequenceIncrementing
-
- isOn() - Method in class OutputSequenceIndexed
-
- isOutline() - Method in class ColoredBase
-
If true, an outline is drawn around the entries.
- isOutlineAtBoundary() - Method in class Outline
-
- isOutputEnabled() - Method in class CSVWriter
-
- isOutputEnabled(String) - Method in class All
-
- isOutputEnabled(String) - Method in class IgnoreUnderscorePrefix
-
- isOutputEnabled(String) - Method in class None
-
- isOutputEnabled(String) - Method in class SpecificDisabled
-
- isOutputEnabled(String) - Method in class SpecificEnabled
-
- isOutputEnabled(String) - Method in class MultiLevelBinary
-
- isOutputEnabled(String) - Method in class MultiLevelNot
-
- isOutputEnabled(String) - Method in class OutputEnabledMutable
-
- isOutputEnabled(String) - Method in class SingleLevelBinary
-
- isOutputEnabled(String) - Method in class SingleLevelInSet
-
- isOutputEnabled(String) - Method in class SingleLevelNot
-
- isOutputEnabled(String) - Method in interface SingleLevelOutputEnabled
-
Is a particular a particular output-enabled?
- isOutputIncrementingNumberSequence() - Method in class OutputPrefixerSettings
-
Requests outputting with an incrementing number sequence, rather than the usual outputter
(normally based upon input filenames).
- isOutputShort() - Method in class GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- isOutsideAtThreshold() - Method in class OutlineKernelBase
-
- isOutsideOffUnignored() - Method in class KernelApplicationParameters
-
- isOutsideOffUnignored() - Method in class KernelPointCursor
-
- isOutsideOn() - Method in class KernelApplicationParameters
-
- isOutsideOn() - Method in class KernelPointCursor
-
- isOutsideOn() - Method in enum OutsideKernelPolicy
-
- isOutsideOnUnignored() - Method in class KernelApplicationParameters
-
- isParamPrefixAppendNumber() - Method in class PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- isPhysical() - Method in class UnitConverter
-
- isPlateau(int) - Method in class EncodedVoxels
-
- isPlayloadUsed() - Method in class MergePairs
-
- isPlayloadUsed() - Method in class MergeToIncreaseObjectFeature
-
- isPlayloadUsed() - Method in class MergeWithFeature
-
Is the payload considered in making decisions? (iff false, payload of nodes is irrelvant)
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>) - Static method in class VisitSchedulerConvexAboutRoot
-
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>, boolean) - Static method in class VisitSchedulerConvexAboutRoot
-
- isPointInside(Point3d) - Method in class Ellipse
-
- isPointInside(Point3d) - Method in class Ellipsoid
-
- isPointInside(Point3d) - Method in class MarkWithPositionAndSingleRadius
-
- isPointInside(Point3d) - Method in class Mark
-
- isPointInside(Point3d) - Method in class LineSegment
-
- isPointInside(Point3d) - Method in class PointList
-
- isPointInside(Point3d) - Method in class Polygon
-
- isPointInside(Point3d) - Method in class PolygonCurve
-
- isPointInside(Point3d) - Method in class RotatableBoundingBox
-
- isPointInside(DrawOverlay, Point3i) - Method in class OverlayMark
-
- isPointInside(DrawOverlay, Point3i) - Method in class OverlayObjectMask
-
- isPointInside(DrawOverlay, Point3i) - Method in class Overlay
-
Is a point inside an overlay? (for a particular OverlayWriter).
- isPointOn(Point3i) - Method in class Mask
-
- isPointOnMask(Point3d, EnergyStack, Function<Point3d, Point3i>) - Method in class CheckMarkWithMask
-
- isPrefix() - Method in class FromXmlList
-
If true, a prefix is prepended to the name of each added bean.
- isPreserveAspectRatio() - Method in class ToDimensions
-
If true, the ratio between x and y is kept constant when scaling.
- isPreserveExtensionIfDuplicate() - Method in class RemoveExtension
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another
- isPreventObjectIntersection() - Method in class EdgeAdderParameters
-
Iff true, objects can only be neighbors if they have no intersecting voxels.
- isProposal() - Method in class VoxelizedMarksPeriodicReporter
-
- isProposed() - Method in class KernelDescision
-
- isRadiusInMeters() - Method in class WithRadiusBase
-
- isRecordedAsEnabled(String) - Method in class RecordedOutputs
-
Is a particular output-name recorded as enabled?
- isRecurseSubfolders() - Method in class MultiFileReader
-
- isRecursive() - Method in class SearchDirectory
-
If true the search is applied recursively over sub-directories.
- isRecursive() - Method in class ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- isRejectIterationIfAllLow() - Method in class Erode
-
- isRejectIterationIfDisconnected() - Method in class Erode
-
- isRelationToValueTrue(double, double) - Method in class EqualTo
-
- isRelationToValueTrue(double, double) - Method in class GreaterThan
-
- isRelationToValueTrue(double, double) - Method in class GreaterThanEqualTo
-
- isRelationToValueTrue(double, double) - Method in class LessThan
-
- isRelationToValueTrue(double, double) - Method in class LessThanEqualTo
-
- isRelationToValueTrue(double, double) - Method in interface RelationToValue
-
- isRelativeForIdentifier() - Method in class InputArguments
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- isRelativeForIdentifier() - Method in class InputContextParams
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- isRelativeToDirectory() - Method in class FileNamerContext
-
If true, the namer should prefer to derive file-names relative to the directory, rather than
only the varying elements in the file-names.
- isRemoveExtension() - Method in class FilePathPattern
-
if true, the extension is removed from paths before finding the pattern.
- isRemoveExtensionInDescription() - Method in class LastDirectories
-
Whether to remove the file-extension from the filename.
- isRemoveTouchingBorderXY() - Method in class FeatureCostAssigner
-
- isReplaceMatchesWithSolids() - Method in class CompareAnnotations
-
- isReplaceWithMidpoint() - Method in class MergeGreedyToIncreaseObjectFeature
-
- isReportFitterErrors() - Method in class FitPoints
-
- isRequireAllFilesMatch() - Method in class GroupFiles
-
- isRequireBBoxNeighbors() - Method in class MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or
touch
- isRequireTouching() - Method in class MergeWithFeature
-
Requires the object-masks to touch.
- isResultUnusual(double) - Method in class ReplaceInfinity
-
- isResultUnusual(double) - Method in class ReplaceNaN
-
- isResultUnusual(double) - Method in class ReplaceUnusualValue
-
- isRewardHigherSide() - Method in class GaussianCumulative
-
Treat the higher side as if it's the the fill cdf
- isRewardLowerSide() - Method in class GaussianCumulative
-
- isRGB() - Method in class DisplayStack
-
- isRGB() - Method in class Stack
-
If true, and the stack has exactly three channels, this stack can be interpreted as a RGB
image.
- isRGB() - Method in interface NamedChannelsForSeries
-
Whether the channels describe an RGB image.
- isRGB() - Method in class NamedChannelsForSeriesConcatenate
-
- isRGB() - Method in class NamedChannelsForSeriesMap
-
- isRGB() - Method in interface OpenedImageFile
-
- isRGB() - Method in class ScaleableBackground
-
- isRgb() - Method in class StackWriteAttributes
-
Whether it's an RGB image when it has three channels (the three channels visualized jointly, rather than independently)
- isRGB(IFormatReader) - Method in class Default
-
- isRGB(IFormatReader) - Method in class ForceBitsPerPixel
-
- isRGB(IFormatReader) - Method in class ForceNumberChannels
-
- isRGB(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- isRGB(IFormatReader) - Method in class ReadOptions
-
Is it an image with three channels (red, green and blue)?
- isRGB(IFormatReader) - Method in class ReadOptionsDelegate
-
- isRGB(IFormatReader) - Method in class SwitchChannelTime
-
- isRGB() - Method in class BioformatsOpenedRaster
-
- isRgb() - Method in class FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- isRGB() - Method in class MultiFileReaderOpenedRaster
-
- isRootInStructure() - Method in class ExperimentResultsExperimentStructure
-
If true the directory structure is
ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory
structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- isScaleLabel() - Method in class TileWithLabels
-
- isSecond() - Method in class ExperimentIdentifierAuto
-
Only relevant if time==true.
- isSecondary() - Method in class VoxelizedMarksPeriodicReporter
-
If proposal is true, this toggles between the primary and secondary proposal
- isSelective() - Method in class OutputPattern
-
Whether the output should be checked to see if it is allowed or not.
- isSeparateEachLabel() - Method in class SuppressNonMaxima
-
If true, each label is reduced separately.
- isShowAgg() - Method in class MemoryUsageReporter
-
- isShowBest() - Method in class MemoryUsageReporter
-
- isShowDomainAxis() - Method in class BarPlot
-
- isShowVerticalAxisLines() - Method in class PlotInstance
-
- isShuffle() - Method in class InputArguments
-
If true, the order of the inputs are shuffled (randomized).
- isShuffle() - Method in class InputContextParams
-
If true, the order of the inputs are shuffled (randomized).
- isSigmaInMeters() - Method in class BlurStrategy
-
- isSilentlyDeleteExisting() - Method in class OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an
error.
- isSingleChannel() - Method in class StackWriteAttributes
-
The number of channels is guaranteed to be 1 in the output.
- isSkipAtBorder() - Method in class FillHoles
-
If true we do not fill any objects that touch the border
- isSkipFileName() - Method in class LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- isSkipFileName() - Method in class FilePathAppendBase
-
- isSkipMissingChannels() - Method in class NamedChannelsAppend
-
- isSlicesSeparately() - Method in class FitBoxToOnVoxels
-
- isStackAsChannel() - Method in class MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no
additionalChannel is set)
- isStackBackground() - Method in class VisualizeOnBackground
-
- isStrongEdgeEnhancer() - Method in class AnisotropicDiffusion
-
Enables the StrongEdgeEnhancer diffusion function
- isSubtractFromMaskOnly() - Method in class SubtractMean
-
- isSuppress3D() - Method in class MorphologicalOperatorBase
-
- isSuppress3D() - Method in class SurfaceNumberVoxelsBase
-
- isSuppress3D() - Method in class SegmentThresholdAboveMinBound
-
- isSuppressDirectories() - Method in class FromDescriptiveName
-
If true, any directory separators in the identifier in a descriptive-name are replaced by
underscores.
- isSuppressErrors() - Method in class FromObjects
-
- isSuppressExceptions() - Method in class JobProcessor
-
- isSuppressExceptions() - Method in class ParametersUnbound
-
- isSuppressExceptions() - Method in class QuickMultiDatasetExperiment
-
- isSuppressExceptions() - Method in class QuickMultiDatasetStructuredExperiment
-
- isSuppressOutlineZ() - Method in class ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- isSuppressRes() - Method in class RadiiRatio
-
- isSuppressRootOut() - Method in class Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against
the location of the BeanXML.
- isSuppressSeries() - Method in class ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- isSuppressSubfolders() - Method in class DefineOutputter
-
- isSuppressZ() - Method in class BoundingBoxIntersection
-
- isSuppressZ() - Method in class DistanceTransform3D
-
- isSuppressZ() - Method in class DistanceTransformForEachObject3D
-
- isSuppressZ() - Method in class MergeWithOptionalDistanceConstraint
-
- isSuppressZ() - Method in class CostOverlapWithinMidpointDistance
-
- isSuppressZ() - Method in class ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- isSuppressZ() - Method in class CenterOnMask
-
- isSuppressZ() - Method in class UniformRandom
-
- isSuppressZ() - Method in class SurfaceSizeMaskNonZero
-
- isSuppressZ() - Method in class EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- isSuppressZCovariance() - Method in class FromObjects
-
- isSuppressZCovariance() - Method in class LinearLeastSquaresEllipsoidFitter
-
- isTemporary(int) - Method in class EncodedIntBuffer
-
- isTemporary(int) - Method in class EncodedVoxels
-
- isTestBothDirections() - Method in class EdgeAdderParameters
-
iff true each combination of neighbors is tested only once, otherwise twice
- isThreeChannels() - Method in class StackWriteAttributes
-
The number of channels is guaranteed to be 3 in the output.
- isThrowExceptionForInsufficientPoints() - Method in class CreateMarkFromPoints
-
- isThumbnailsEnabled() - Method in class InputProcessContext
-
- isTime() - Method in class ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output
- isTransposed() - Method in class CombineCSV
-
- isTrue(ObjectWithProperties, RGBStack, int) - Method in interface IfElse.Condition
-
- isUnchanged(double, int) - Method in class UnchangedBase
-
Whether the current value is unchanged compared to the previous value.
- isUnchanged(double, int) - Method in class UnchangedScore
-
- isUnchanged(double, int) - Method in class UnchangedSize
-
- isUniformlySized() - Method in class StackNotUniformSized
-
- isUniformTyped() - Method in class StackNotUniformSized
-
- isUnsigned() - Method in class FloatVoxelType
-
- isUnsigned() - Method in class SignedVoxelType
-
- isUnsigned() - Method in class UnsignedVoxelType
-
- isUnsigned() - Method in class VoxelDataType
-
- isUnstarted() - Method in class JobState
-
- isUnvisited(int) - Method in class EncodedIntBuffer
-
- isUnvisited(int) - Method in class EncodedVoxels
-
- isUseLastSeriesIndexOnly() - Method in class NamedChannels
-
- isUseLastSeriesIndexOnly() - Method in class Stacks
-
- isUseMax() - Method in class OverlapRatio
-
- isUseMax() - Method in class OverlapRatioMask
-
- isUseMIP() - Method in class MultipleComparer
-
- isUseMIP() - Method in class CompareAnnotations
-
- isUseZ() - Method in class KernelApplicationParameters
-
Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
- isUseZ() - Method in class KernelPointCursor
-
- isUseZ() - Method in class RemoveTouchingBorder
-
- isUseZ() - Method in class TraverseOutlineOnImage
-
- isValidName(String) - Static method in class RGBChannelNames
-
Whether the channel-name is one of red, green, or blue.
- isVaryColors() - Method in class SegmentInstanceWithModel
-
If true the colors change for different objects in the image (using a default color set).
- iterateBins(Histogram.BinConsumer) - Method in class Histogram
-
Calls consumer for every bin-value, increasing from min to max.
- iterateBinsUntil(int, Histogram.BinConsumer) - Method in class Histogram
-
Calls consumer for every bin-value until a limit, increasing from min to limit
(inclusive).
- IterateKernelHelper - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel
-
Routines to iterate a kernel over a set of points in a
BinaryVoxels.
- iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class FunctionalIterate
-
Iterate through all entries in a
Map.
- iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface SliceBufferIndex
-
Calls sliceConsumer once for each slice with the respective buffer
- iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface SliceBufferIndex
-
Calls process for each offset in each slice
- iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXY(PointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class Extent
-
Calls processor once for each x and y-values but only passing an offset.
- iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range, with a shift added.
- iterateOverZ(CheckedIntConsumer<E>) - Method in class Extent
-
Calls processor once for each z-value in the range
- iterateOverZUntil(IntPredicate) - Method in class Extent
-
Calls processor once for each z-value in the range unless indexPredicate returns
false.
- IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over
all voxels in one or more
Voxels.
- IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of image voxels within a bounding-box.
- IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator
-
- IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask
-
Utilities for iterating over the subset of voxels corresponding to an
on state in a
Mask.
- IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor
-
Utilities for iterating over the neighboring voxels to a given point.
- IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an
on state in an
ObjectMask.
- IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an
on state in an
optional
ObjectMask.
- IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over
remaining voxels in one or more
VoxelBuffers.
- iterator() - Method in class SequenceInteger
-
An iterator for each element in the sequence
- iterator() - Method in class StringList
-
- iterator() - Method in class StringSet
-
- iterator() - Method in class ColorList
-
- iterator() - Method in class NameValueSet
-
- iterator() - Method in class ConcurrentJobMonitor
-
- iterator() - Method in class FeatureList
-
- iterator() - Method in class CombinedName
-
- iterator() - Method in class SimpleName
-
- iterator() - Method in class FeatureNameList
-
- iterator() - Method in class ResultsVectorList
-
- iterator() - Method in class CacheTransferSourceCollection
-
- iterator() - Method in class SharedFeatureMulti
-
- iterator() - Method in class NamedFeatureStore
-
- iterator() - Method in class BoundingBoxesOnPlane
-
- iterator() - Method in class ObjectCollectionWithProperties
-
- iterator() - Method in class SeedCollection
-
- iterator() - Method in class Stack
-
- iterator() - Method in class StackNotUniformSized
-
- iterator() - Method in class TimeSequence
-
- iterator() - Method in class StackSeries
-
- iterator() - Method in class ObjectCollection
-
- iterator() - Method in class VoxelsWrapperList
-
- iterator() - Method in class InputsWithDirectory
-
- iterator() - Method in class EnergySavedInd
-
- iterator() - Method in class EnergySchemeSet
-
- iterator() - Method in class MemoList
-
- iterator() - Method in class UpdatableMarksList
-
- iterator() - Method in class ColoredMarks
-
- iterator() - Method in class MarkCollection
-
- iterator() - Method in class WeightedKernelList
-
- iterator() - Method in class ColoredOverlayCollection
-
- iterator() - Method in class OverlayCollection
-
- iterator() - Method in class OverlayProperties
-
- iterator() - Method in class AnnotationGroupList
-
- iterator() - Method in class LevelResultCollection
-
- iterator() - Method in class ParsedFilePathBag
-
- iterator() - Method in class SortedSetChannel
-
- iteratorCoupledManifests() - Method in class ManifestCouplingDefinition
-
- iteratorCoupledManifestsFor(Manifest) - Method in class ManifestCouplingDefinition
-
- iteratorExperimentalManifests() - Method in class ManifestCouplingDefinition
-
- iteratorFromRaster() - Method in class NamedChannelsForSeriesConcatenate
-
- ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
- ObjectAggregationBase() - Constructor for class ObjectAggregationBase
-
- ObjectAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
Writes an object-mask as a mask (i.e.
- ObjectAsMaskGenerator() - Constructor for class ObjectAsMaskGenerator
-
Creates using a default image-resolution.
- ObjectAsMaskGenerator(Optional<Resolution>) - Constructor for class ObjectAsMaskGenerator
-
- ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- ObjectAsPoints() - Constructor for class ObjectAsPoints
-
- ObjectCollection - Class in org.anchoranalysis.image.voxel.object
-
- ObjectCollection() - Constructor for class ObjectCollection
-
Creates with no objects
- ObjectCollection(Stream<ObjectMask>) - Constructor for class ObjectCollection
-
Creates with elements from a stream
- ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object
-
- ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider
-
- ObjectCollectionProvider() - Constructor for class ObjectCollectionProvider
-
- ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
- ObjectCollectionProviderFilterBase() - Constructor for class ObjectCollectionProviderFilterBase
-
- ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
- ObjectCollectionProviderMorphological() - Constructor for class ObjectCollectionProviderMorphological
-
- ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider
-
- ObjectCollectionProviderUnary() - Constructor for class ObjectCollectionProviderUnary
-
- ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
- ObjectCollectionProviderWithFeature() - Constructor for class ObjectCollectionProviderWithFeature
-
- ObjectCollectionReader - Class in org.anchoranalysis.image.io.object.input
-
- ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
- ObjectCollectionWithProperties() - Constructor for class ObjectCollectionWithProperties
-
- ObjectCollectionWithProperties(ObjectMask) - Constructor for class ObjectCollectionWithProperties
-
- ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class ObjectCollectionWithProperties
-
- ObjectCollectionWithProperties(ObjectCollection) - Constructor for class ObjectCollectionWithProperties
-
- ObjectCollectionWithPropertiesFactory - Class in org.anchoranalysis.image.core.object.properties
-
- ObjectCollectionWriter - Class in org.anchoranalysis.image.io.object.output.hdf5
-
- ObjectComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
-
An object-collection to be used to compare against something
- ObjectComparer() - Constructor for class ObjectComparer
-
- objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in class Base
-
- objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface VoxelsExtracter
-
Copies an area corresponding to an object-mask to another
Voxels
- ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer
-
A means of extracting attributes associated with a particular object (e.g.
- ObjectDrawAttributes(ColorIndex) - Constructor for class ObjectDrawAttributes
-
Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
- ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class ObjectDrawAttributes
-
- ObjectDrawAttributesFactory - Class in org.anchoranalysis.overlay.writer
-
- ObjectFilter - Class in org.anchoranalysis.image.bean.object
-
- ObjectFilter() - Constructor for class ObjectFilter
-
- ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
A filter that combines other filters (in a list)
- ObjectFilterCombine() - Constructor for class ObjectFilterCombine
-
- ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
Uses a predicate to make a decision whether to keep objects or not.
- ObjectFilterPredicate() - Constructor for class ObjectFilterPredicate
-
- ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
An independent object-filter that uses a relation in its predicate.
- ObjectFilterRelation() - Constructor for class ObjectFilterRelation
-
- objectFor(T) - Method in interface AccessObjectMask
-
An object-mask for a given element.
- ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
-
- ObjectInputStreamDeserializer() - Constructor for class ObjectInputStreamDeserializer
-
- ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
-
- ObjectMask - Class in org.anchoranalysis.image.voxel.object
-
An object expressed in voxels, bounded within overall space.
- ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
Creates an object-mask with a corner at the origin (i.e.
- ObjectMask(BoundingBox) - Constructor for class ObjectMask
-
Creates an object-mask to corresponding to a bounding-box with all pixels off (0)
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
Creates an object-mask to correspond to bounded-voxels.
- ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class ObjectMask
-
- ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge
-
Merges one or more
ObjectMasks into a single object
- ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object
-
A custom "stream" like class for various functional-programming operations on
ObjectCollection
- ObjectMaskStream(ObjectCollection) - Constructor for class ObjectMaskStream
-
- ObjectMatcher - Class in org.anchoranalysis.image.bean.object
-
Matches an object with other objects.
- ObjectMatcher() - Constructor for class ObjectMatcher
-
- ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
-
- ObjectOutputStreamGenerator() - Constructor for class ObjectOutputStreamGenerator
-
- ObjectOutputStreamGenerator(Optional<String>) - Constructor for class ObjectOutputStreamGenerator
-
- ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ObjectRadiusStandardDeviation() - Constructor for class ObjectRadiusStandardDeviation
-
- objects() - Method in class ImageInitialization
-
- objects() - Method in class MultiInput
-
- OBJECTS - Static variable in class OutputterDirectories
-
Where collections of objects are typically placed in a define-experiment output
- objects(String) - Static method in class ReferenceFactory
-
- OBJECTS_ROOT - Static variable in class HDF5PathHelper
-
Hardcoded string that identifies in the HDF5 file for where the object-collection is stored
- OBJECTS_ROOT_WITH_SEPERATORS - Static variable in class HDF5PathHelper
-
Adds seperators before and after the OBJECTS_ROOT_PATH
- objectsAreAllInside(Extent) - Method in class ObjectCollection
-
- ObjectsAsGrayscaleGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Base class for generators that accept a set of objects as input.
- ObjectsAsGrayscaleGenerator(Dimensions) - Constructor for class ObjectsAsGrayscaleGenerator
-
- ObjectsAsRGBGenerator - Class in org.anchoranalysis.image.io.object.output.rgb
-
A base class for generators that draw objects on top of a RGB-Stack.
- ObjectsAsRGBGenerator(DrawObject, ObjectDrawAttributes, Either<Dimensions, DisplayStack>) - Constructor for class ObjectsAsRGBGenerator
-
- ObjectsAsUniqueValueGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Writes objects as a Raster with unique id values for each object.
- ObjectsAsUniqueValueGenerator(Dimensions) - Constructor for class ObjectsAsUniqueValueGenerator
-
- ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- ObjectSerializerPeriodicReporter(String) - Constructor for class ObjectSerializerPeriodicReporter
-
- objectsForThumbnail(T) - Method in class CombineObjectsForFeatures
-
Selects objects from an input that will be used for thumbnail generation
- objectsForThumbnail(FeatureInputSingleObject) - Method in class EachObjectIndependently
-
- objectsForThumbnail(FeatureInputPairObjects) - Method in class PairNeighbors
-
- ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.binary.connected
-
Creates a
ObjectCollection from the connected-components of a mask or binary-voxels.
- ObjectsFromConnectedComponentsFactory() - Constructor for class ObjectsFromConnectedComponentsFactory
-
- ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class ObjectsFromConnectedComponentsFactory
-
- ObjectsFromConnectedComponentsFactory(int) - Constructor for class ObjectsFromConnectedComponentsFactory
-
- ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class ObjectsFromConnectedComponentsFactory
-
- objectsFromOverlays(OverlayCollection) - Static method in class OverlayCollectionObjectFactory
-
Creates objects from whatever Overlays are found in the collection *
- ObjectsMergedAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Writes objects merged together as a mask.
- ObjectsMergedAsMaskGenerator(Dimensions) - Constructor for class ObjectsMergedAsMaskGenerator
-
- ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
-
- ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class ObjectsToCompare
-
- objectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator
-
The objects to draw (without any colors) on the background
- objectsToDraw(Dimensions) - Method in class ColoredObjects
-
- objectsToDraw(Dimensions) - Method in class ColoredMarks
-
- ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge
-
A vertex in a merge graph representing an object (and and an associated payload)
- ObjectVertex(ObjectMask, double) - Constructor for class ObjectVertex
-
- ObjectWithBoundingBoxGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
- ObjectWithBoundingBoxGenerator(Optional<Resolution>) - Constructor for class ObjectWithBoundingBoxGenerator
-
- ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
-
- ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class ObjectWithEllipse
-
- ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature-value from a collection.
- ObjectWithMaximumFeature() - Constructor for class ObjectWithMaximumFeature
-
- ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature among a group of matches for each object.
- ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
An
ObjectMask with associated key-value properties.
- ObjectWithProperties(BoundingBox) - Constructor for class ObjectWithProperties
-
- ObjectWithProperties(ObjectMask) - Constructor for class ObjectWithProperties
-
- ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class ObjectWithProperties
-
- obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class AggregateTriggerBank
-
- obtain(int, PeriodReceiver<S>) - Method in class PeriodTriggerBank
-
- of(Stream<T>) - Static method in class FunctionalList
-
Creates a list from a stream.
- of(boolean, boolean) - Static method in enum OutsideKernelPolicy
-
Multiplexes between all three possible enums.
- of(boolean) - Static method in class NeighborhoodFactory
-
Gets an appropriate neighborhood
- of(ObjectMask...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list
- of(ObjectCollection...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections
- of(Optional<ObjectCollection>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections (if they exist)
- of(Collection<ObjectMask>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections
- of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list of
BinaryVoxels
converting the voxels in their entireity to an object-mask at the origin.
- of(CalculationResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class CalculateShellObjectMask
-
- of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateDilation
-
- of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
-
- of(SessionInput<FeatureInputSingleObject>, boolean) - Static method in class CalculateEllipsoidLeastSquares
-
- offset(int, int) - Method in class Dimensions
-
- offset(Point3i) - Method in class Dimensions
-
- offset(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- offset(int, int) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
- offset(int, int, int) - Method in class Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
- offset(ReadableTuple3i) - Method in class Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
- offset(Point2i) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
- offsetGlobal(int, int) - Method in class ObjectMask
-
- offsetRelative(int, int) - Method in class ObjectMask
-
- offsetSlice(Point3i) - Method in class Dimensions
-
- offsetSlice(ReadableTuple3i) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
- OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
- OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer
-
- ofResolved(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
-
- OMETiff - Class in org.anchoranalysis.io.bioformats.bean.writer
-
- OMETiff() - Constructor for class OMETiff
-
Default constructor.
- OMEXML - Class in org.anchoranalysis.io.bioformats.bean.writer
-
- OMEXML() - Constructor for class OMEXML
-
Default constructor.
- One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects one specific channel from a set of stacks
- One() - Constructor for class One
-
- oneOnly(String, String, boolean, boolean) - Static method in class CheckMisconfigured
-
Checks that one of two properties is defined, but not both simultaneously (exclusive OR).
- OneOrThreeChannelsWriter - Class in org.anchoranalysis.image.io.bean.stack.writer
-
A base-class for a raster-writer that writes only one or three channeled images, and a flexible
extension.
- OneOrThreeChannelsWriter() - Constructor for class OneOrThreeChannelsWriter
-
- OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
-
- OneStageGenerator() - Constructor for class OneStageGenerator
-
- ongoingTasksLessThan(int) - Method in class ConcurrentJobMonitor
-
- onInit(P) - Method in class InitializableBean
-
Called after initialization.
- onInit(NullInitialization) - Method in class NullParamsBean
-
- onInit() - Method in class NullParamsBean
-
As there's no parameters we expose a different method
- onInit(DictionaryInitialization) - Method in class DictionaryProviderReference
-
- onInit(FeatureInitialization) - Method in class Feature
-
Called after initialization.
- onInit(FeaturesInitialization) - Method in class ReferencedFeatures
-
- onInit(ImageInitialization) - Method in class BinarySegmentationReference
-
- onInit() - Method in class MarkWithIdentifierFactory
-
- onInit(ImageInitialization) - Method in class FromInput
-
- onInit(ImageInitialization) - Method in class FromChannel
-
- onInit(ImageInitialization) - Method in class Reference
-
- onInit(ImageInitialization) - Method in class FromStackChannel
-
- onInit(ImageInitialization) - Method in class ReferenceOrElse
-
- onInit(ImageInitialization) - Method in class FromInput
-
- onInit(FeaturesInitialization) - Method in class PermuteFeature
-
- onInit(MarksInitialization) - Method in class FeatureValueCheckMark
-
- onInit(MarksInitialization) - Method in class MarkProposerReference
-
- onInit(MarksInitialization) - Method in class MarkMergeProposerReference
-
- onInit(MarksInitialization) - Method in class MarkSplitProposerReference
-
- onInit(MarksInitialization) - Method in class KernelMerge
-
- onInit(PointsInitialization) - Method in class Reference
-
- OnlyIf - Class in org.anchoranalysis.experiment.bean.log
-
Logs messages to a particular location ONLY if certain conditions are fulfilled.
- OnlyIf() - Constructor for class OnlyIf
-
- open() - Method in interface Progress
-
- open() - Method in class ProgressConsole
-
- open() - Method in class ProgressIgnore
-
- open() - Method in class ProgressIncrement
-
- open() - Method in class ProgressOneOfMany
-
- open(int, Progress) - Method in interface OpenedImageFile
-
Open when we don't have a specific-type
- open(int, Progress) - Method in class BioformatsOpenedRaster
-
- open(Path) - Static method in class CSVReaderByLine
-
Default reader, using comma and first-line headers
- open(Path, String, boolean) - Static method in class CSVReaderByLine
-
Default reader, using comma and first-line headers
- open(Path, String, boolean, boolean) - Static method in class CSVReaderByLine
-
Default reader, using comma and first-line headers
- open(int, Progress) - Method in class MultiFileReaderOpenedRaster
-
- openCheckType(int, Progress, VoxelDataType) - Method in interface OpenedImageFile
-
- OpenCVReader - Class in org.anchoranalysis.plugin.opencv.bean.stack
-
Reads a stack from the file-system using OpenCV.
- OpenCVReader() - Constructor for class OpenCVReader
-
- OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.stack
-
Writes a stack to the file-system using OpenCV and a specified extension.
- OpenCVWriter() - Constructor for class OpenCVWriter
-
- OpenedCSVFile() - Constructor for class CSVReader.OpenedCSVFile
-
- OpenedImageFile - Interface in org.anchoranalysis.image.io.stack.input
-
An image file that has been opened for reading containing one or more series of image-
Stacks.
- openFile(Path) - Method in class StackReader
-
Opens a file containing one or more images but does not read an image.
- openFile(Path) - Method in class BioformatsReader
-
- openFile(Path) - Method in class BranchExtension
-
- openFile(Path) - Method in class FlattenAsChannel
-
- openFile(Path) - Method in class ImposeResolution
-
- openFile(Path) - Method in class MultiFileReader
-
- openFile(Path) - Method in class ReadVoxelExtentXml
-
- openFile(Path) - Method in class RejectIfConditionXYResolution
-
- openFile(Path) - Method in class OpenCVReader
-
- openMarksFromFilePath(Path) - Static method in class TestLoaderMarks
-
- openMarksFromTestPath(String) - Method in class TestLoaderMarks
-
- openMask(StackReader, Path, BinaryValues) - Static method in class MaskReader
-
Utility functions for opening a single-channeled stack as a
Mask.
- openXmlAbsoluteFilePath(String) - Static method in class TestLoader
-
Opens a XML document - with an absolute path on the filesystem
- openXmlAbsoluteFilePath(Path) - Static method in class TestLoader
-
Opens a XML document - with an absolute path on the filesystem
- openXmlFromTestPath(String) - Method in class TestLoader
-
Opens a XML document - with a path relative to the test root
- OperationFailedException - Exception in org.anchoranalysis.core.exception
-
- OperationFailedException(String) - Constructor for exception OperationFailedException
-
- OperationFailedException(Throwable) - Constructor for exception OperationFailedException
-
- OperationFailedException(String, Throwable) - Constructor for exception OperationFailedException
-
- OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception
-
- OperationFailedRuntimeException(String) - Constructor for exception OperationFailedRuntimeException
-
- OperationFailedRuntimeException(Exception) - Constructor for exception OperationFailedRuntimeException
-
- OperationMap<T> - Class in org.anchoranalysis.mpp.io.input
-
Stores objects as operations
- OperationMap() - Constructor for class OperationMap
-
- OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
-
- OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class OptimizationContext
-
- OptimizationScheme<S,U,V> - Class in org.anchoranalysis.mpp.segment.bean.optimization
-
An optimization-scheme that uses kernels to make changes to state.
- OptimizationScheme() - Constructor for class OptimizationScheme
-
- OptimizationStep<S,T,V> - Class in org.anchoranalysis.mpp.segment.optimization.step
-
- OptimizationStep() - Constructor for class OptimizationStep
-
- OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- OptimizationStepLogReporter() - Constructor for class OptimizationStepLogReporter
-
- OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
-
- OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception OptimizationTerminatedEarlyException
-
- OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must
always have a non-null value.
- OptionalFactory - Class in org.anchoranalysis.bean
-
Utility functions to create
Optional from nullable providers or boolean flags.
- OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined
-
A simple container expressing a value and an associationed optional name.
- OptionalNameValue(Optional<String>, V) - Constructor for class OptionalNameValue
-
- OptionalOperationUnsupportedException - Exception in org.anchoranalysis.core.exception
-
- OptionalOperationUnsupportedException() - Constructor for exception OptionalOperationUnsupportedException
-
- OptionalOperationUnsupportedException(String) - Constructor for exception OptionalOperationUnsupportedException
-
- OptionalOperationUnsupportedException(Exception) - Constructor for exception OptionalOperationUnsupportedException
-
- OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
-
- OptionalUtilities - Class in org.anchoranalysis.core.functional
-
Additional utility functions for
Optional and exceptions.
- or(StackWriteAttributes) - Method in class StackWriteAttributes
-
- Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the
result.
- Or() - Constructor for class Or
-
- Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical OR i.e.
- Or() - Constructor for class Or
-
- order(String) - Method in interface OrderProvider
-
- OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
-
- OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- OrderedList() - Constructor for class OrderedList
-
- orderedListOfFeatures() - Method in class AddCriteriaEnergyPair
-
- orderedListOfFeatures() - Method in class AddCriteriaNever
-
- orderedListOfFeatures() - Method in class AddCriteriaOr
-
- orderedListOfFeatures() - Method in class ArbitraryPointCommon
-
- orderedListOfFeatures() - Method in class BoundingBoxIntersection
-
- orderedListOfFeatures() - Method in interface OrderedFeatureList
-
A list of features used to determine the add-criteria, or null if irrelevant.
- orderedListOfFeatures() - Method in class AddCriteriaFeatureRelationThreshold
-
- OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
- OrderedRadius() - Constructor for class OrderedRadius
-
- OrderProvider - Interface in org.anchoranalysis.core.index.bounded
-
- orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class OptionalUtilities
-
- orElseGetFlat(Optional<T>, CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities
-
- orFlat(CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- org.anchoranalysis.annotation - package org.anchoranalysis.annotation
-
Ground truth for an image in diverse forms.
- org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image
-
Annotations that apply to an image as a whole.
- org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io
-
Reading and writing annotations to the filesystem.
- org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment
-
A pairing of objects from two collections (bipartite matching).
- org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator
-
Generates output images to illustrate a
Assignment between annotations.
- org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean
-
Beans related to reading / writing / specifying annotations.
- org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer
-
What to compare an annotation (ground truth) against?
- org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image
-
Reading and writing whole-image label annotations.
- org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable
-
The outcome of searching for annotations or images on the file-system.
- org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark
-
Reading and writing
Mark-related annotations from/to the
file-system.
- org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark
-
Annotations that use one or more marks to describe entities in an image.
- org.anchoranalysis.bean - package org.anchoranalysis.bean
-
- org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation
-
- org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define
-
- org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder
-
- org.anchoranalysis.bean.exception - package org.anchoranalysis.bean.exception
-
Exceptions that can occur executing generic operations on
Anchor Beans.
- org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable
-
Initializing beans with particular parameters, including recursively.
- org.anchoranalysis.bean.initializable.params - package org.anchoranalysis.bean.initializable.params
-
Some kinds of parameters used when initializing beans.
- org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property
-
Performing initializion on particular properties in a bean.
- org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute
-
Applying permutations to a bean's fields.
- org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property
-
Applying permutations to the properties of a bean.
- org.anchoranalysis.bean.permute.setter - package org.anchoranalysis.bean.permute.setter
-
Setter used to impose a permutation on bean properties.
- org.anchoranalysis.bean.provider - package org.anchoranalysis.bean.provider
-
A means of creating / loading / referencing a bean from another bean or class.
- org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared
-
Utility beans which have a generally broader use than a specific module.
- org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color
-
Beans that specify colors.
- org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme
-
Beans that create lists or indices of colors according to particular schemes.
- org.anchoranalysis.bean.shared.dictionary - package org.anchoranalysis.bean.shared.dictionary
-
Setting, referencing and initializing key-value parameters.
- org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path
-
Defines a root path directory on the filesystem whre files are read / written.
- org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random
-
Specifies a particular type of random-number generator.
- org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex
-
Specifies regular-expressions.
- org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation
-
Specifies a binary relation of some kind between scalars.
- org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold
-
Specifies a unary relation to a *threshold* value.
- org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml
-
Reading Beans from XML files.
- org.anchoranalysis.bean.xml.exception - package org.anchoranalysis.bean.xml.exception
-
Exceptions that can thrown when loading beans from XML.
- org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory
-
Custom factories for loading beans in custom ways from XML.
- org.anchoranalysis.browser.launcher - package org.anchoranalysis.browser.launcher
-
Launching the anchor GUI interactive application from command-line.
- org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache
-
Caching (memozing) calls to a method so an operation does not need to be repeated.
- org.anchoranalysis.core.color - package org.anchoranalysis.core.color
-
Specifying particular colors and groups of colors.
- org.anchoranalysis.core.concurrency - package org.anchoranalysis.core.concurrency
-
Specifying how many CPUs and GPUs can be allocated for some purpose.
- org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception
-
Very general exceptions and base classes for exceptions with wide applicability.
- org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable
-
Nested exceptions of similar type that can be combined together in a summary.
- org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly
-
Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly
error descriptions.
- org.anchoranalysis.core.format - package org.anchoranalysis.core.format
-
File formats and associated extensions.
- org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional
-
Utilities and interfaces for applying functional-programming.
- org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked
-
Versions of many functional-interfaces in java.util.function that throw
checked-exceptions.
- org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph
-
Data-structures for directed and undirected graphs, with or without an edge payload.
- org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter
-
Data structures for adding a unique name (a String or integer identifier) to other entities.
- org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name
-
Data structures for name (String) and value associations.
- org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider
-
A collection of named-elements, a
NamedProvider, and related operations.
- org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store
-
Data structures like
NamedProvider with
supporting for adding new elements.
- org.anchoranalysis.core.index - package org.anchoranalysis.core.index
-
Classes to support getting/setting/specifying unique-integers (indices) for elements.
- org.anchoranalysis.core.index.bounded - package org.anchoranalysis.core.index.bounded
-
A range of elements with indiced, bounded to lie between particular a minimum and maximum.
- org.anchoranalysis.core.index.bounded.bridge - package org.anchoranalysis.core.index.bounded.bridge
-
- org.anchoranalysis.core.log - package org.anchoranalysis.core.log
-
Interfaces to log messages, both information and error messages.
- org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error
-
Mechanism for reporting errors (exceptions/throwables) to the user.
- org.anchoranalysis.core.progress - package org.anchoranalysis.core.progress
-
Classes to allow for tracking the progress of a task that can be broken into smaller units, for
reporting to the user.
- org.anchoranalysis.core.random - package org.anchoranalysis.core.random
-
Generating random numbers.
- org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize
-
Utilities for serializing and deserializing objects.
- org.anchoranalysis.core.system - package org.anchoranalysis.core.system
-
Utilities for interacting with the operating system or computer system generally
- org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path
-
Utilities for converting/manipulating file-paths.
- org.anchoranalysis.core.value - package org.anchoranalysis.core.value
-
Encapsulating values or sets of named-values.
- org.anchoranalysis.experiment - package org.anchoranalysis.experiment
-
Classes related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.arguments - package org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment in addition to its bean specification.
- org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean
-
Beans related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier
-
Assigning unique names to experiments.
- org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io
-
Generic experiments that handle input and output in structured ways.
- org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log
-
Different approaches to where messages on the progress/status of an experiment are logged to.
- org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor
-
How a task is executed on multiple inputs.
- org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require
-
A test whether certain conditions on arguments to experiments are fulfilled.
- org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task
-
Defines a
task,
which is a set of operations run on an input, that may or may not generate an output.
- org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io
-
Interfaces for replacing attributes of an experiment: input, output, task etc.
- org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log
-
Helpful classes for logging.
- org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task
-
Non-bean classes related to a
Task.
- org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor
-
- org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean
-
Beans pertaining to feature-calculation.
- org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list
-
A feature-list (custom list type for features) and associated providers.
- org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator
-
Features that are sufficiently generic to work on any input-type.
- org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider
-
Provider of a single feature.
- org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results
-
- org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate
-
Sub-feature units of calculation that can be cached.
- org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache
-
Classes to cache feature-results or parts of feature-results that occur repeatedly among features
or across calculations of the same feature.
- org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy
-
A particular stack used in feature-calculations called a
EnergyStack together with related classes.
- org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input
-
Base classes providing inputs to feature calculations.
- org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv
-
Writing feature calculation-results in CSV format.
- org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name
-
Naming items in a weay that breaks down into multiple elements.
- org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results
-
Writes feature-calculation results in different formats, also grouped results.
- org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group
-
Various different outputs that can be written for the a grouped version of the results in
ResultsWriter.
- org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name
-
Data objects for the names of features.
- org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results
-
Results from one or more feature calculations.
- org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session
-
A defined context in which one or more features are provided inputs and produce results.
- org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache
-
- org.anchoranalysis.feature.session.cache.finder - package org.anchoranalysis.feature.session.cache.finder
-
Strategies to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
- org.anchoranalysis.feature.session.calculator.multi - package org.anchoranalysis.feature.session.calculator.multi
-
Calculates results for one or more features for a given input.
- org.anchoranalysis.feature.session.calculator.single - package org.anchoranalysis.feature.session.calculator.single
-
Calculates results for a single feature for a given input.
- org.anchoranalysis.feature.session.replace - package org.anchoranalysis.feature.session.replace
-
Strategies on whether to reuse or invalidate a feature-input's cache.
- org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared
-
Features shared for referencing among calculations.
- org.anchoranalysis.feature.store - package org.anchoranalysis.feature.store
-
- org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean
-
Core (bean) classes for image processing.
- org.anchoranalysis.image.bean.channel.converter - package org.anchoranalysis.image.bean.channel.converter
-
Base classes for comparing a channel to another type.
- org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator
-
Beans for specifying image interpolators.
- org.anchoranalysis.image.bean.nonbean.error - package org.anchoranalysis.image.bean.nonbean.error
-
Specific exception types that can be thrown in this module.
- org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init
-
Initialization of image-related beans.
- org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment
-
Non-bean classes relating to image-segmentation.
- org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
Non-beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object
-
Beans pertaining to
ObjectMask and their
collections.
- org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider
-
Base classes for providers of different core data entities related to images.
- org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack
-
- org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment
-
Base classes to perform image segmentation, transforming an image into another meaningful entity
or entities.
- org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary
-
Base classes to perform binary-segmentation.
- org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object
-
Base classes to segment a channel into objects.
- org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial
-
Beans to define entities or operate that consider Euclidian space.
- org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange
-
Beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction
-
Beans to specify a direction.
- org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold
-
Base classes for thresholding and calculating levels for thresholding.
- org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation
-
Reusable relations to a threshold.
- org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance
-
Converting quantities of distance between units.
- org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent
-
Converting quantities of extent (area or volume) between units.
- org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area
-
Converting quantities of area between units.
- org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume
-
Converting quantities of volume between units.
- org.anchoranalysis.image.core.bufferedimage - package org.anchoranalysis.image.core.bufferedimage
-
- org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel
-
The
Channel core data-class and related operations
and converters.
- org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert
-
Converts a channel to other data-types.
- org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached
-
Converts a channel to another data-type based upon another object to which it is attached.
- org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel
-
Converts a channel to another data-type based upon a
Channel to which it is
attached.
- org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram
-
Converts a channel to another data-type based upon a
Histogram to which it is
attached.
- org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory
-
Factory classes for creating
Channel for various
voxel data-types.
- org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions
-
Classes to describe the size of images or components of images both in voxels and physically.
- org.anchoranalysis.image.core.dimensions.size - package org.anchoranalysis.image.core.dimensions.size
-
Determining or changing the size of an image.
- org.anchoranalysis.image.core.dimensions.size.suggestion - package org.anchoranalysis.image.core.dimensions.size.suggestion
-
Suggestions on a size for an image.
- org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask
-
An image with only two permissible states.
- org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine
-
Binary operations involving voxelwise combination of
Mask.
- org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge
-
Merges two or more entities.
- org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object
-
The key data entity org.anchoranalysis.image.voxel.object and related-classes and
operations.
- org.anchoranalysis.image.core.object.factory - package org.anchoranalysis.image.core.object.factory
-
- org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label
-
Labelling elements (object-masks or similar) with unique successive integers in a channel.
- org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties
-
- org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale
-
Scaling object-collections, or lists of elements with object-representations.
- org.anchoranalysis.image.core.object.seed - package org.anchoranalysis.image.core.object.seed
-
Starting points for segmentation that are guaranteed to lie on one distinct object.
- org.anchoranalysis.image.core.orientation - package org.anchoranalysis.image.core.orientation
-
Various methods to specify the orientation (general direction) of an entity.
- org.anchoranalysis.image.core.outline - package org.anchoranalysis.image.core.outline
-
Finds outline voxels, the pixels on the contour/edge of the object.
- org.anchoranalysis.image.core.outline.traverser - package org.anchoranalysis.image.core.outline.traverser
-
Performs a walk on every voxel on the outline of an object-mask.
- org.anchoranalysis.image.core.outline.traverser.distance - package org.anchoranalysis.image.core.outline.traverser.distance
-
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
- org.anchoranalysis.image.core.outline.traverser.path - package org.anchoranalysis.image.core.outline.traverser.path
-
A set of contiguously neighboring points along the outline of an object.
- org.anchoranalysis.image.core.outline.traverser.path.merge - package org.anchoranalysis.image.core.outline.traverser.path.merge
-
- org.anchoranalysis.image.core.outline.traverser.path.merge.strategy - package org.anchoranalysis.image.core.outline.traverser.path.merge.strategy
-
- org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points
-
Operations that extract points from image data entities or vice versa.
- org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack
-
Defines the key data object,
Stack, and related
classes.
- org.anchoranalysis.image.core.stack.named - package org.anchoranalysis.image.core.stack.named
-
A collection of
Stacks, each with a unique identifier
as a name.
- org.anchoranalysis.image.core.stack.time - package org.anchoranalysis.image.core.stack.time
-
- org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean
-
Beans pertaining to feature definition and calculation.
- org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator
-
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
- org.anchoranalysis.image.feature.bean.histogram - package org.anchoranalysis.image.feature.bean.histogram
-
- org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection
-
- org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair
-
- org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single
-
- org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical
-
Features that convert to/from physical spatial units (e.g.
- org.anchoranalysis.image.feature.calculation - package org.anchoranalysis.image.feature.calculation
-
- org.anchoranalysis.image.feature.calculator - package org.anchoranalysis.image.feature.calculator
-
Implementations of
FeatureCalculatorMulti related to images,
especially to create tables of feature-calculations.
- org.anchoranalysis.image.feature.calculator.merged - package org.anchoranalysis.image.feature.calculator.merged
-
A particular implementation of
FeatureCalculatorMulti for
feature-calculations based upon pairs of image-objects.
- org.anchoranalysis.image.feature.input - package org.anchoranalysis.image.feature.input
-
- org.anchoranalysis.image.io - package org.anchoranalysis.image.io
-
Reading and writing of image-related data objects to and from the filesystem.
- org.anchoranalysis.image.io.bean.channel - package org.anchoranalysis.image.io.bean.channel
-
Beans pertaining to reading
Channels as input.
- org.anchoranalysis.image.io.bean.object.draw - package org.anchoranalysis.image.io.bean.object.draw
-
How to represent an object-mask in a raster that is being drawn.
- org.anchoranalysis.image.io.bean.object.feature - package org.anchoranalysis.image.io.bean.object.feature
-
- org.anchoranalysis.image.io.bean.stack.combine - package org.anchoranalysis.image.io.bean.stack.combine
-
Beans to combine multiple stacks into a single stack before outputting.
- org.anchoranalysis.image.io.bean.stack.reader - package org.anchoranalysis.image.io.bean.stack.reader
-
Bean classes for reading raster-files from the filesystem.
- org.anchoranalysis.image.io.bean.stack.writer - package org.anchoranalysis.image.io.bean.stack.writer
-
Bean classes for writing raster-files to the filesystem.
- org.anchoranalysis.image.io.channel.input - package org.anchoranalysis.image.io.channel.input
-
Non-bean classes for reading a
Channel from the
filesystem.
- org.anchoranalysis.image.io.channel.input.series - package org.anchoranalysis.image.io.channel.input.series
-
Non-bean classes for reading a
series of Channels from the filesystem.
- org.anchoranalysis.image.io.channel.output - package org.anchoranalysis.image.io.channel.output
-
Non-bean classes for writing a
Channel to the
filesystem.
- org.anchoranalysis.image.io.histogram.input - package org.anchoranalysis.image.io.histogram.input
-
Non-bean classes for reading a
Histogram from the
filesystem.
- org.anchoranalysis.image.io.histogram.output - package org.anchoranalysis.image.io.histogram.output
-
Non-bean classes for writing a
Histogram to the
filesystem.
- org.anchoranalysis.image.io.object - package org.anchoranalysis.image.io.object
-
Non-bean classes for reading / writing an
ObjectCollection from and to the filesystem.
- org.anchoranalysis.image.io.object.input - package org.anchoranalysis.image.io.object.input
-
- org.anchoranalysis.image.io.object.output.grayscale - package org.anchoranalysis.image.io.object.output.grayscale
-
- org.anchoranalysis.image.io.object.output.hdf5 - package org.anchoranalysis.image.io.object.output.hdf5
-
- org.anchoranalysis.image.io.object.output.mask - package org.anchoranalysis.image.io.object.output.mask
-
Writing an
ObjectCollection to the filesystem as
multiple binary singled-channeled images.
- org.anchoranalysis.image.io.object.output.rgb - package org.anchoranalysis.image.io.object.output.rgb
-
- org.anchoranalysis.image.io.stack - package org.anchoranalysis.image.io.stack
-
Non-bean classes for reading / writing a
Stack from
and to the filesystem.
- org.anchoranalysis.image.io.stack.input - package org.anchoranalysis.image.io.stack.input
-
Non-bean classes for reading a
Stack from the
filesystem.
- org.anchoranalysis.image.io.stack.output - package org.anchoranalysis.image.io.stack.output
-
Non-bean classes for writing a
Stack to the
filesystem.
- org.anchoranalysis.image.io.stack.output.box - package org.anchoranalysis.image.io.stack.output.box
-
Base classes for generators that ultimately write
only a bounding-box portion of a
Stack to the filesystem.
- org.anchoranalysis.image.io.stack.output.generator - package org.anchoranalysis.image.io.stack.output.generator
-
Base classes for generators that ultimately write a
Stack to the filesystem.
- org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel
-
Data-structures to store and manipulate image raster-data or voxels.
- org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic
-
Arithmetic operations for
Voxels.
- org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner
-
Assigns values to some or all voxels.
- org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary
-
- org.anchoranalysis.image.voxel.binary.connected - package org.anchoranalysis.image.voxel.binary.connected
-
- org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values
-
Defining on and off intensity-values to interpret an image in a binary way.
- org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer
-
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels.
- org.anchoranalysis.image.voxel.buffer.max - package org.anchoranalysis.image.voxel.buffer.max
-
- org.anchoranalysis.image.voxel.buffer.mean - package org.anchoranalysis.image.voxel.buffer.mean
-
Buffer for performing a mean intensity projection.
- org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive
-
Conversion of both primitive data types and image structures between Anchor's data-structures and
other representations.
- org.anchoranalysis.image.voxel.buffer.slice - package org.anchoranalysis.image.voxel.buffer.slice
-
A container with voxel-buffers for each z-slice.
- org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert
-
Converting
Voxels to different data-types.
- org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2
-
Converts anchor data-structures to those used by
ImgLib2.
- org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype
-
The different data-types that can be used to represent voxels.
- org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter
-
Methods to read/copy/duplicate portions of voxels.
- org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate
-
Methods to find or count voxels that satisfy a predicate.
- org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory
-
- org.anchoranalysis.image.voxel.interpolator - package org.anchoranalysis.image.voxel.interpolator
-
Different interpolator methods to use when scaling voxels.
- org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator
-
Utilities to iterate over voxel-locations in images and sub-regions of images.
- org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting
-
Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over
the intersecting regions of two entities.
- org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor
-
Iterating over a point's neighboring voxels.
- org.anchoranalysis.image.voxel.iterator.neighbor.kernel - package org.anchoranalysis.image.voxel.iterator.neighbor.kernel
-
- org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate
-
Functional-interfaces for processing different combinations of points and buffers that return a
boolean.
- org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process
-
Functional-interfaces for processing different combinations of points and buffers that do not
return a value.
- org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer
-
Functional-interfaces for processing different combinations of points and raw buffers, but not
VoxelBuffer.
- org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Functional-interfaces for processing different combinations of points and
VoxelBuffer but not raw buffers.
- org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel
-
Applying a
kernel via
convolution to voxels.
- org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count
-
Kernels to count the number of voxels that are equal to a particular value.
- org.anchoranalysis.image.voxel.kernel.morphological - package org.anchoranalysis.image.voxel.kernel.morphological
-
Kernels that apply morphological operations.
- org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline
-
Kernel to find outline voxels on an object.
- org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood
-
A region in proximity to a voxel, encompassing this voxel as well as others.
- org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object
-
The fundamental data class that is an
ObjectMask
and related structures.
- org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological
-
- org.anchoranalysis.image.voxel.object.morphological.predicate - package org.anchoranalysis.image.voxel.object.morphological.predicate
-
Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
- org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics
-
Statistics about aggregated voxel intensities.
- org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder
-
Thresholding operations on voxels.
- org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats
-
Non-bean classes for filesystem I/O using
Bioformats.
- org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean
-
- org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options
-
User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
- org.anchoranalysis.io.bioformats.bean.writer - package org.anchoranalysis.io.bioformats.bean.writer
-
Writing stacks to the file system using the Bioformats library.
- org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert
-
Converts the byte stream opened by Bioformats into channels of particular data-type.
- org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte
-
Converts the byte stream opened by Bioformats into channels of
ByteBuffer.
- org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat
-
Converts the byte stream opened by Bioformats into channels of
FloatBuffer.
- org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint
-
Converts the byte stream opened by Bioformats into channels of
IntBuffer.
- org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort
-
Converts the byte stream opened by Bioformats into channels of
ShortBuffer.
- org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator
-
Base-classes and utilities for generators, which write different types of objects to the file
system.
- org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection
-
Outputting more than one element collectively using a generator.
- org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined
-
Combining multiple generators into one.
- org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence
-
Writing a sequence of elements using a generator.
- org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern
-
A particular naming pattern files follow when outputted.
- org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized
-
Generators for writing serialized objects.
- org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular
-
Generators for writing tabular data, including CSV.
- org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text
-
Generators for writing textual data, including strings.
- org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml
-
Generators for writing XML data.
- org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer
-
Raster-writers that use ImageJ to write images to the filesystem.
- org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert
-
Converts to and from ImageJ data-structures for images.
- org.anchoranalysis.io.input - package org.anchoranalysis.io.input
-
Classes relating to creating inputs for an experiment / task.
- org.anchoranalysis.io.input.bean - package org.anchoranalysis.io.input.bean
-
Beans related to collecting inputs from the file-system for an experiment.
- org.anchoranalysis.io.input.bean.dictionary - package org.anchoranalysis.io.input.bean.dictionary
-
- org.anchoranalysis.io.input.bean.files - package org.anchoranalysis.io.input.bean.files
-
Methods to provide a collection of
Files.
- org.anchoranalysis.io.input.bean.namer - package org.anchoranalysis.io.input.bean.namer
-
Beans to derive names (compact unique identifiers) from files.
- org.anchoranalysis.io.input.bean.path - package org.anchoranalysis.io.input.bean.path
-
Beans pertaining to manipulating and matching against file-paths.
- org.anchoranalysis.io.input.bean.path.matcher - package org.anchoranalysis.io.input.bean.path.matcher
-
Beans to find a subset of files that match a particular conditions on their paths.
- org.anchoranalysis.io.input.bean.path.provider - package org.anchoranalysis.io.input.bean.path.provider
-
Methods to provide a single file-path.
- org.anchoranalysis.io.input.csv - package org.anchoranalysis.io.input.csv
-
Classes for reading comma-separated-values (CSV) files.
- org.anchoranalysis.io.input.file - package org.anchoranalysis.io.input.file
-
Non-bean classes that relate to using files during inputting.
- org.anchoranalysis.io.input.path - package org.anchoranalysis.io.input.path
-
Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
- org.anchoranalysis.io.input.path.matcher - package org.anchoranalysis.io.input.path.matcher
-
Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.
- org.anchoranalysis.io.manifest - package org.anchoranalysis.io.manifest
-
A manifest that records what outputs occur and where they occur.
- org.anchoranalysis.io.manifest.deserializer - package org.anchoranalysis.io.manifest.deserializer
-
Classes to read manifests from the file-system.
- org.anchoranalysis.io.manifest.directory - package org.anchoranalysis.io.manifest.directory
-
Entities to indicate a directory in the manifest.
- org.anchoranalysis.io.manifest.directory.sequenced - package org.anchoranalysis.io.manifest.directory.sequenced
-
Classes related to a directory that has a particular sequence of outputted filenames.
- org.anchoranalysis.io.manifest.file - package org.anchoranalysis.io.manifest.file
-
Entities to indicate a file and its role in the manifest.
- org.anchoranalysis.io.manifest.finder - package org.anchoranalysis.io.manifest.finder
-
Methods to search through a manifest-file to find outputs matching certain conditions.
- org.anchoranalysis.io.manifest.finder.match - package org.anchoranalysis.io.manifest.finder.match
-
Predicates that are useful for matching against particular type of objects in finders.
- org.anchoranalysis.io.manifest.operationrecorder - package org.anchoranalysis.io.manifest.operationrecorder
-
Makes a record of each file/subdirectory written as output.
- org.anchoranalysis.io.manifest.sequencetype - package org.anchoranalysis.io.manifest.sequencetype
-
Predictable patterns of indexes as used in sets of outputted files.
- org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean
-
Beans for the framework around writing files to the file-system.
- org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled
-
Beans indicating whether a particular output is enabled or not.
- org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer
-
Beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules
-
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
- org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled
-
Non-beans pertaining to whether a particular output is enabled or not.
- org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi
-
Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
- org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single
-
Non-beans that pertain to whether a single level has outputs that are enabled or not.
- org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error
-
Exceptions that may be thrown when writing files to the file-system.
- org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle
-
Methods of naming a file with an index in the file-name.
- org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter
-
Classes for outputting to particular directories.
- org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory
-
BoundDirectory and related classes.
- org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer
-
Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded
-
Classes for recording the output-names used as they are written / queried.
- org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer
-
Allows a generators to write element(s) to the filesystem.
- org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml
-
Outputting XML to the file-system.
- org.anchoranalysis.launcher - package org.anchoranalysis.launcher
-
Parent package and entry-point classes for the Anchor command-line launcher application.
- org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config
-
Specifies a configuration of the launcher for a particular application.
- org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor
-
Runs a particular experiment after identifying necessary paths and input files.
- org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam
-
Different methods of selecting a object T that is used as a parameter for an experiment.
- org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment
-
- org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParams for loading a
Optional<Path> for inputs, outputs or tasks.
- org.anchoranalysis.launcher.executor.selectparam.path.convert - package org.anchoranalysis.launcher.executor.selectparam.path.convert
-
Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
- org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options
-
A centralized location for all command-line options used by the launcher.
- org.anchoranalysis.launcher.options.process - package org.anchoranalysis.launcher.options.process
-
Adding/removing/changing the arguments (input and output) from the experiment via
command-line-options.
- org.anchoranalysis.launcher.resources - package org.anchoranalysis.launcher.resources
-
Reading and integrating resources for the launcher.
- org.anchoranalysis.launcher.run - package org.anchoranalysis.launcher.run
-
Parses command-line arguments and runs an experiment.
- org.anchoranalysis.launcher.run.tasks - package org.anchoranalysis.launcher.run.tasks
-
Loading and displaying pre-defined tasks.
- org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic
-
Performing primitive type conversion, counting and summing.
- org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation
-
Solving or manipulating equations.
- org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram
-
The
Histogram data class and related operations.
- org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization
-
- org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation
-
Different kinds of binary-relations.
- org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics
-
Data structures and algorithms to calculate statistics.
- org.anchoranalysis.math.statistics.moment - package org.anchoranalysis.math.statistics.moment
-
Calculates first and second
image
moments from a covariance matrix of points.
- org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean
-
- org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound
-
Lower and upper limits set around variables.
- org.anchoranalysis.mpp.bean.bound.rotation - package org.anchoranalysis.mpp.bean.bound.rotation
-
Bounds on how to rotate an entity in Euclidean space.
- org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark
-
Beans generally related to
Marks.
- org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory
-
Beans related to creating
Marks.
- org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points
-
Operations based on sets of points.
- org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter
-
Fitting structures to sets of points.
- org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer
-
Proposing
Marks or other data-structures with particular
attributes.
- org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider
-
- org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap
-
Voxel subregions of
Marks.
- org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria
-
- org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element
-
- org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme
-
- org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark
-
- org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection
-
- org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy
-
- org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks
-
- org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved
-
- org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme
-
- org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error
-
- org.anchoranalysis.mpp.feature.input.memo - package org.anchoranalysis.mpp.feature.input.memo
-
- org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark
-
- org.anchoranalysis.mpp.index - package org.anchoranalysis.mpp.index
-
Indexing voxel-values in different ways.
- org.anchoranalysis.mpp.index.factory - package org.anchoranalysis.mpp.index.factory
-
Factories for classes in org.anchoranalysis.mpp.index.
- org.anchoranalysis.mpp.init - package org.anchoranalysis.mpp.init
-
Parameters used to initialize certain types of beans.
- org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input
-
- org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature
-
- org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input
-
- org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks
-
- org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator
-
- org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output
-
- org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark
-
Non-bean classes related to
Marks.
- org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic
-
- org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points
-
Marks implementing structures based on points.
- org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized
-
A mark after a voxel-representation has been inferred.
- org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo
-
- org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap
-
Calculating overlaps between two
Marks.
- org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay
-
- org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair
-
- org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer
-
Non-bean classes for proposing
Marks or other data-structures
with particular attributes.
- org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error
-
Recording errors related to proposing
Marks or other
data-structures with particular attributes.
- org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean
-
Beans for segmentation algorithms related to marked-point-processes.
- org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define
-
- org.anchoranalysis.mpp.segment.bean.kernel - package org.anchoranalysis.mpp.segment.bean.kernel
-
Base classes for kernels that transition a configuration of marks (a
MarkCollection) into an altered version.
- org.anchoranalysis.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.mpp.segment.bean.kernel.proposer
-
- org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization
-
- org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
- org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination
-
- org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define
-
- org.anchoranalysis.mpp.segment.kernel - package org.anchoranalysis.mpp.segment.kernel
-
- org.anchoranalysis.mpp.segment.kernel.proposer - package org.anchoranalysis.mpp.segment.kernel.proposer
-
- org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization
-
- org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback
-
- org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period
-
- org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step
-
- org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer
-
- org.anchoranalysis.overlay - package org.anchoranalysis.overlay
-
Overlays and related classes involving drawing entities on top
of an image.
- org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean
-
Beans relating to drawing an
Overlay on an image.
- org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection
-
- org.anchoranalysis.overlay.identifier - package org.anchoranalysis.overlay.identifier
-
- org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object
-
- org.anchoranalysis.overlay.object.scaled - package org.anchoranalysis.overlay.object.scaled
-
Creates a scaled version of
ObjectMask to use as an
overlay.
- org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer
-
Drawing an overlay on an image.
- org.anchoranalysis.plot - package org.anchoranalysis.plot
-
Plotting data on charts.
- org.anchoranalysis.plot.bean - package org.anchoranalysis.plot.bean
-
Beans for plotting.
- org.anchoranalysis.plot.bean.colorscheme - package org.anchoranalysis.plot.bean.colorscheme
-
Color schemes associated with plots.
- org.anchoranalysis.plot.index - package org.anchoranalysis.plot.index
-
Non-bean plot definitions.
- org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate
-
Beans to combine two or more annotations.
- org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer
-
Comparing the similarity of annotations from two images to each other.
- org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison
-
Task to compare a set of annotations to a segmentation or another set of annotations.
- org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner
-
Pairs annotations from two different sets, creating an assignment of some type.
- org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file
-
- org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label
-
A label as used for annotating.
- org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy
-
Strategies for how to annotate an image, such label per image etc.
- org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison
-
Non-bean classes for comparing two sets of annotations.
- org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
-
Morphological grayscale-reconstruction algorithm.
- org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider
-
- org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
- org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define
-
- org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider
-
- org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold
-
- org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur
-
Filters that perform blurring.
- org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert
-
- org.anchoranalysis.plugin.image.bean.channel.convert.histogram - package org.anchoranalysis.plugin.image.bean.channel.convert.histogram
-
- org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider
-
- org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
- org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
- org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
- org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
- org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask
-
- org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object
-
- org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score
-
- org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
- org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider
-
- org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider
-
- org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider
-
- org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold
-
- org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider
-
- org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
- org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert
-
- org.anchoranalysis.plugin.image.bean.mask.provider.dimensions - package org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
-
- org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
- org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
- org.anchoranalysis.plugin.image.bean.mask.provider.resize - package org.anchoranalysis.plugin.image.bean.mask.provider.resize
-
- org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
- org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice
-
- org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter
-
- org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine
-
- org.anchoranalysis.plugin.image.bean.object.filter.dependent - package org.anchoranalysis.plugin.image.bean.object.filter.dependent
-
- org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent
-
- org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match
-
- org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider
-
- org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected
-
- org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature
-
- org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter
-
- org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask
-
- org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge
-
- org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
- org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment
-
- org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice
-
- org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
-
- org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Strategies for reducing the number of elements with a list by merging/removing lower-confidence
elements that overlap.
- org.anchoranalysis.plugin.image.bean.object.segment.stack - package org.anchoranalysis.plugin.image.bean.object.segment.stack
-
Instance-segmentation of a
Stack.
- org.anchoranalysis.plugin.image.bean.params - package org.anchoranalysis.plugin.image.bean.params
-
- org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale
-
Implementations of
ScaleCalculator for calculating
a scaling-factor from dimensions.
- org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary
-
- org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider
-
- org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color
-
- org.anchoranalysis.plugin.image.bean.stack.provider.plot - package org.anchoranalysis.plugin.image.bean.stack.provider.plot
-
- org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object
-
- org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
- org.anchoranalysis.plugin.image.box - package org.anchoranalysis.plugin.image.box
-
Non-beans pertaining to bounding-boxes.
- org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel
-
- org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions
-
- org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
-
- org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute
-
- org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological
-
- org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection
-
- org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine
-
- org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair
-
- org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
-
- org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
- org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical
-
- org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score
-
- org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared
-
- org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object
-
- org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
- org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object
-
- org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object
-
- org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
- org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation
-
- org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity
-
- org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level
-
- org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object
-
- org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge
-
- org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition
-
- org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority
-
- org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider
-
- org.anchoranalysis.plugin.image.segment - package org.anchoranalysis.plugin.image.segment
-
- org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding
-
- org.anchoranalysis.plugin.image.task.bean - package org.anchoranalysis.plugin.image.task.bean
-
A parent package for many different kinds of tasks.
- org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature
-
- org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source
-
Source of rows in feature-tables with
FeatureSource and derived classes.
- org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format
-
Tasks for converting image-formats.
- org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Different approaches for converting sets of channels (RGB, independently etc.) to another image
format.
- org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped
-
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
- org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram
-
Task(s) to export histograms of intensity values.
- org.anchoranalysis.plugin.image.task.bean.grouped.raster - package org.anchoranalysis.plugin.image.task.bean.grouped.raster
-
Task(s) to calculate the mean of channels grouped together.
- org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selecting a subset of a set of channels.
- org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller
-
Associating labels with images.
- org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale
-
Tasks to scale an image.
- org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment
-
Tasks to segment an image.
- org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice
-
Tasks that process on one or more slices from a z-stack.
- org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature
-
Non-bean classes pertaining to
Features as used in tasks.
- org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator
-
Non-beans for calculating
Features.
- org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped
-
Non-bean classes about grouping channels or other inputs.
- org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller
-
Non-bean classes about labelling images.
- org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment
-
Non-bean classes for image-segmentation.
- org.anchoranalysis.plugin.image.task.stack - package org.anchoranalysis.plugin.image.task.stack
-
Non-bean classes pertaining to stacks and channels as used in tasks.
- org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail
-
Non-bean classes for thumbnail creation.
- org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
-
- org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define
-
- org.anchoranalysis.plugin.imagej.bean.interpolator - package org.anchoranalysis.plugin.imagej.bean.interpolator
-
- org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider
-
- org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider
-
- org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment
-
- org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider
-
- org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold
-
- org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider
-
- org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask
-
- org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map
-
- org.anchoranalysis.plugin.io.bean.file.copy.method - package org.anchoranalysis.plugin.io.bean.file.copy.method
-
- org.anchoranalysis.plugin.io.bean.file.copy.naming - package org.anchoranalysis.plugin.io.bean.file.copy.naming
-
- org.anchoranalysis.plugin.io.bean.file.group - package org.anchoranalysis.plugin.io.bean.file.group
-
- org.anchoranalysis.plugin.io.bean.file.group.check - package org.anchoranalysis.plugin.io.bean.file.group.check
-
- org.anchoranalysis.plugin.io.bean.file.group.parser - package org.anchoranalysis.plugin.io.bean.file.group.parser
-
- org.anchoranalysis.plugin.io.bean.file.namer - package org.anchoranalysis.plugin.io.bean.file.namer
-
- org.anchoranalysis.plugin.io.bean.file.namer.patternspan - package org.anchoranalysis.plugin.io.bean.file.namer.patternspan
-
- org.anchoranalysis.plugin.io.bean.file.path - package org.anchoranalysis.plugin.io.bean.file.path
-
- org.anchoranalysis.plugin.io.bean.file.path.prefixer - package org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
- org.anchoranalysis.plugin.io.bean.file.provider - package org.anchoranalysis.plugin.io.bean.file.provider
-
- org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input
-
- org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel
-
- org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files
-
- org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider
-
- org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter
-
- org.anchoranalysis.plugin.io.bean.input.manifest - package org.anchoranalysis.plugin.io.bean.input.manifest
-
- org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack
-
- org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive
-
- org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader
-
- org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer
-
- org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer
-
- org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image
-
- org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input
-
- org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path
-
- org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task
-
- org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter
-
- org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path
-
- org.anchoranalysis.plugin.io.manifest - package org.anchoranalysis.plugin.io.manifest
-
- org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile
-
- org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer
-
- org.anchoranalysis.plugin.io.shared - package org.anchoranalysis.plugin.io.shared
-
Objects used in shared-state in tasks.
- org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml
-
Reading and writing metadata XML.
- org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier
-
Beans that perform classification in some way.
- org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster
-
Beans that perform clustering in some way.
- org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria
-
- org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound
-
- org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check
-
- org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define
-
- org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider
-
- org.anchoranalysis.plugin.mpp.bean.outline - package org.anchoranalysis.plugin.mpp.bean.outline
-
- org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge
-
- org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points
-
- org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
-
- org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline - package org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
-
- org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position
-
- org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii
-
- org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split
-
- org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single
-
- org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region
-
- org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary
-
- org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider
-
- org.anchoranalysis.plugin.mpp.experiment - package org.anchoranalysis.plugin.mpp.experiment
-
- org.anchoranalysis.plugin.mpp.experiment.bean - package org.anchoranalysis.plugin.mpp.experiment.bean
-
- org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature - package org.anchoranalysis.plugin.mpp.experiment.bean.feature
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.report - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
-
- org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects
-
- org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment
-
- org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects
-
- org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit
-
- org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap
-
- org.anchoranalysis.plugin.mpp.segment - package org.anchoranalysis.plugin.mpp.segment
-
- org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
-
- org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner
-
- org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater
-
- org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization
-
- org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv
-
- org.anchoranalysis.plugin.opencv.bean.color - package org.anchoranalysis.plugin.opencv.bean.color
-
Operations involving color-spaces and OpenCV.
- org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature
-
Extracting features using OpenCV.
- org.anchoranalysis.plugin.opencv.bean.object.segment.decode.instance - package org.anchoranalysis.plugin.opencv.bean.object.segment.decode.instance
-
Decoding the tensor output from inference into an instance segmentation.
- org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Segmentation of a
Stack using OpenCV.
- org.anchoranalysis.plugin.opencv.bean.stack - package org.anchoranalysis.plugin.opencv.bean.stack
-
- org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert
-
Conversion to/from OpenCV data-structures.
- org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean
-
Features that combine or convert other features in a generic way.
- org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
Arithmetic involving features.
- org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional
-
Conditional operations involving features.
- org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list
-
Operations that extract a single value from a list of features.
- org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range
-
Features that compare against a range of values.
- org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace
-
Replaces particular values if they are returned from a feature.
- org.anchoranalysis.plugin.operator.feature.bean.statistics - package org.anchoranalysis.plugin.operator.feature.bean.statistics
-
Converts feature values based upon a statistical measure of distribution.
- org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical
-
Converting to/from physical units.
- org.anchoranalysis.plugin.operator.feature.statistics - package org.anchoranalysis.plugin.operator.feature.statistics
-
Non-bean statistical operations.
- org.anchoranalysis.plugin.points.bean - package org.anchoranalysis.plugin.points.bean
-
Beans that fit or otherwise manipulate sets of points.
- org.anchoranalysis.plugin.points.bean.convexhull - package org.anchoranalysis.plugin.points.bean.convexhull
-
Convex hull operations.
- org.anchoranalysis.plugin.points.bean.feature - package org.anchoranalysis.plugin.points.bean.feature
-
Features related to points and fitting points to conics.
- org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter
-
Fitting geometric structures to points.
- org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse
-
- org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid
-
- org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull
-
Non-bean convex hull operations.
- org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment
-
Quickly defining experiments via several assumptions, including particular file-paths.
- org.anchoranalysis.plugin.quick.bean.file.path.derive - package org.anchoranalysis.plugin.quick.bean.file.path.derive
-
Deriving paths from existing paths as helpful to quickly defined experiments.
- org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input
-
Specifying inputs when quickly defining an experiment.
- org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
Appending other entities to inputs when quickly defining experiments.
- org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure
-
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
- org.anchoranalysis.spatial - package org.anchoranalysis.spatial
-
Classes for geometry or other mathematical operations in Euclidian space.
- org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis
-
Identifying the three standard axes in 3D cartesian coordinates.
- org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box
-
Axis-aligned bounding-boxes and related operations.
- org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point
-
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
- org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer
-
Functional interfaces that accept cartesian coordinate points specified in different ways.
- org.anchoranalysis.spatial.rotation - package org.anchoranalysis.spatial.rotation
-
A matrix to apply a rotation to a point.
- org.anchoranalysis.spatial.rotation.factory - package org.anchoranalysis.spatial.rotation.factory
-
- org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree
-
R-Tree data structure and related operations.
- org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale
-
How to much to scale an entity in Cartesian space by.
- org.anchoranalysis.test - package org.anchoranalysis.test
-
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
- org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment
-
Testing utilities and fixtures with no greater downstream dependency than
anchor-experiment or anchor-mpp or anchor-mpp-io.
- org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher
-
Launches an anchor binary from a shell and runs an experiment.
- org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature
-
Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
- org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins
-
Testing utilities and fixtures with no greater downstream dependency than
anchor-image-feature or anchor-mpp.
- org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature
-
A mocked feature internally using a feature-calculation.
- org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects
-
Fixtures for creating object-masks and related feature-inputs.
- Orientation - Class in org.anchoranalysis.image.core.orientation
-
- Orientation() - Constructor for class Orientation
-
- Orientation - Class in org.anchoranalysis.image.io.bean.object.draw
-
Writes a line through the midpoint illustrating the orientation of the object
- Orientation() - Constructor for class Orientation
-
- Orientation2D - Class in org.anchoranalysis.image.core.orientation
-
- Orientation2D(double) - Constructor for class Orientation2D
-
- Orientation2D() - Constructor for class Orientation2D
-
- Orientation3DEulerAngles - Class in org.anchoranalysis.image.core.orientation
-
- Orientation3DEulerAngles() - Constructor for class Orientation3DEulerAngles
-
- Orientation3DEulerAngles(double, double, double) - Constructor for class Orientation3DEulerAngles
-
- OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
Proposes both an orientation and radii for a
ConicBase
- OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class OrientationAndRadiiProposer
-
- OrientationAxisAngle - Class in org.anchoranalysis.image.core.orientation
-
An orientation in axis-angle representation.
- OrientationAxisAngle(Vector3d, double) - Constructor for class OrientationAxisAngle
-
- OrientationIdentity - Class in org.anchoranalysis.image.core.orientation
-
- OrientationIdentity(int) - Constructor for class OrientationIdentity
-
- OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- OrientationProposer() - Constructor for class OrientationProposer
-
- OrientationRotationMatrix - Class in org.anchoranalysis.image.core.orientation
-
- OrientationRotationMatrix() - Constructor for class OrientationRotationMatrix
-
- OrientationRotationMatrix(RotationMatrix) - Constructor for class OrientationRotationMatrix
-
- otherVertex(V) - Method in class TypedEdge
-
The other vertex on the edge
- Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Performs auto-thresholding using Otsu's method.
- Otsu() - Constructor for class Otsu
-
- OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Similar to Otsu, but weighs the variances differently of background and foreground
- OtsuWeighted() - Constructor for class OtsuWeighted
-
- OtsuWeighted(double, double) - Constructor for class OtsuWeighted
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixer
-
Provides a prefix which can be prepended to all output files.
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class Rooted
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure
-
- outFilePrefixAvoidResolve(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
Provides a prefix which can be prepended to all output files.
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IncrementingNumber
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
Determines the out-file prefix from a path
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class DirectoryStructure
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class FromDescriptiveName
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IfIncrementingNumberRequested
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class LastDirectoryAsPrefix
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathRegEx
-
- outgoingEdgesFor(V) - Method in class GraphWithPayload
-
All outgoing edges for a given vertex.
- outline(Mask, int, boolean, boolean) - Static method in class FindOutline
-
Creates an outline of depth 1 from a mask
- outline(ObjectMask, int, boolean, boolean) - Static method in class FindOutline
-
Creates outline from an object
- Outline - Class in org.anchoranalysis.image.io.bean.object.draw
-
Draws the outline of each object-mask.
- Outline() - Constructor for class Outline
-
- Outline(int) - Constructor for class Outline
-
- Outline(int, boolean) - Constructor for class Outline
-
- Outline - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Always creates a new mask for the result (no need to duplicate input)
- Outline() - Constructor for class Outline
-
- outlineGuess3D(Mask, int, boolean, boolean) - Static method in class FindOutline
-
Finds the outline of a mask, guessing whether to do this in 2D or 3D depending on if the mask
has 3-dimensions
- OutlineKernel - Class in org.anchoranalysis.image.voxel.kernel.outline
-
- OutlineKernel() - Constructor for class OutlineKernel
-
- OutlineKernelBase - Class in org.anchoranalysis.image.voxel.kernel.outline
-
A base class for kernels that find the outline of an
ObjectMask.
- OutlineKernelBase() - Constructor for class OutlineKernelBase
-
- OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
-
- OutlineKernelBase() - Constructor for class OutlineKernelBase
-
- OutlineKernelNeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline
-
Outputs the outline of an object-mask, but only for voxels on the exterior which neighbour a
binary-mask.
- OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class OutlineKernelNeighborMatchValue
-
Creates for an object.
- OutlinePixelsRetriever - Class in org.anchoranalysis.plugin.mpp.bean.outline
-
- OutlinePixelsRetriever() - Constructor for class OutlinePixelsRetriever
-
- OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object
-
Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it
centered in a window of a certain size.
- OutlinePreserveRelativeSize() - Constructor for class OutlinePreserveRelativeSize
-
- outlineSingleColor(int, DisplayStack, RGBColor) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects on a background using a single color for all
objects
- OutlineTraverser - Class in org.anchoranalysis.image.core.outline.traverser
-
- OutlineTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class OutlineTraverser
-
- outlineVariedColors(int, int, DisplayStack) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects on a background using varied colors for the
objects.
- outlineVariedColors(int, int, Either<Dimensions, DisplayStack>) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects on a background using varied colors for the
objects.
- outlineWithColorIndex(int, ColorIndex) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects using a particular color-index.
- output() - Method in class ExecutionArguments
-
Arguments to help specify the outputs from the experiment.
- output(InputOutputContext) - Method in class OutputFeatureTable
-
Outputs the feature-table.
- output(NamedProvider<Stack>, String, boolean, OutputterChecked) - Static method in class NamedStacksOutputter
-
Writes all or a subset from a set of named-stacks to a directory as a raster.
- output(String, boolean) - Method in class NamedProviderOutputter
-
Outputs the entities using a particular output-name.
- OUTPUT_BY_GROUP - Static variable in class CompareAnnotations
-
- OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class ResultsWriterOutputNames
-
If not otherwise specified, the output name for a non-aggregated CSV of the results.
- OUTPUT_FEATURE_TABLE - Static variable in class OutputFeatureTable
-
- OUTPUT_MANIFEST - Static variable in class OutputExperiment
-
- OUTPUT_MANIFEST - Static variable in class Task
-
- OUTPUT_RESULTS - Static variable in class ExportFeatures
-
- OUTPUT_SUMMARY_CSV - Static variable in class SharedStateSegmentInstance
-
- OUTPUT_THUMBNAILS - Static variable in class SharedStateExportFeatures
-
- outputAfterAllTasksAreExecuted(Outputter) - Method in interface ExperimentState
-
- outputAfterAllTasksAreExecuted(Outputter) - Method in class SegmentMarksState
-
- OutputArguments - Class in org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment's output in addition to its bean
specification.
- OutputArguments() - Constructor for class OutputArguments
-
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface ExperimentState
-
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in class SegmentMarksState
-
- OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error
-
When an output-directory already exists.
- OutputDirectoryAlreadyExistsException(String) - Constructor for exception OutputDirectoryAlreadyExistsException
-
- OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Whether a particular output, identified by a textual name, is enabled or not.
- OutputEnabled() - Constructor for class OutputEnabled
-
- OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded
-
Additional output-names to enable or disable from an existing set of output-enabled rules.
- OutputEnabledDelta() - Constructor for class OutputEnabledDelta
-
- OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled
-
A specific set of first-level outputs are enabled, to which more can be added.
- OutputEnabledMutable(String...) - Constructor for class OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules
-
- OutputEnabledRules() - Constructor for class OutputEnabledRules
-
- OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules
-
Base class for an
OutputEnabledRules that specifies particular output-names for first and
second levels.
- OutputEnableRulesSpecify(StringSet) - Constructor for class OutputEnableRulesSpecify
-
Create with a specific set of first-level output names.
- OutputEnableRulesSpecify() - Constructor for class OutputEnableRulesSpecify
-
- OutputExperiment - Class in org.anchoranalysis.experiment.bean.io
-
An experiment that uses a
OutputManager to specify the outputting of results.
- OutputExperiment() - Constructor for class OutputExperiment
-
- OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParam<Path> factory for outputs.
- OutputFeatureTable - Class in org.anchoranalysis.image.io.bean.object.feature
-
Specifies a table of feature-calculations on objects.
- OutputFeatureTable() - Constructor for class OutputFeatureTable
-
- outputFormatString() - Method in class IndexableOutputNameStyle
-
- outputFormatString() - Method in class IntegerSuffixOutputNameStyle
-
- outputFormatString() - Method in class StringSuffixOutputNameStyle
-
- outputGroupedData(ConsistentChannelChecker, InputOutputContext) - Method in class GroupMapByName
-
Outputs the "grouped" data to the filesystem
- outputHeaderToWriter(PrintWriter, String) - Method in class AggIDCounter
-
- outputHeaderToWriter(PrintWriter) - Method in class Aggregator
-
- OutputManager - Class in org.anchoranalysis.io.output.bean
-
Responsible for making decisions on where output goes and what form it takes.
- OutputManager() - Constructor for class OutputManager
-
- outputName(String) - Static method in class FileMatch
-
Match a file whose output-name matches a specific value.
- outputNameForGroups() - Method in class GroupedStackBase
-
The first-level output-name used for determining if groups are written.
- outputNameForGroups() - Method in class ExportImageHistograms
-
- outputNameForGroups() - Method in class GroupedMeanChannelTask
-
- outputNames() - Method in class ResultsWriterMetadata
-
- OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- OutputNameStyle(String) - Constructor for class OutputNameStyle
-
- OutputNameStyle() - Constructor for class OutputNameStyle
-
- OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A particular naming pattern files follow when outputted.
- OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean, Optional<ManifestDescription>) - Constructor for class OutputPattern
-
- OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPattern that outputs a file-name with a trailing integer index.
- OutputPatternIntegerSuffix(String, boolean) - Constructor for class OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
- OutputPatternIntegerSuffix(String, String) - Constructor for class OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the output-name as the subdirectory name, and a specific
prefix.
- OutputPatternIntegerSuffix(String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix
-
- OutputPatternIntegerSuffix(String, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix
-
- OutputPatternIntegerSuffix(String, boolean, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix
-
Creates with a full set of flexibility about how the filename appears and whether a
subdirectory is used.
- OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPattern that outputs a file-name with a trailing string index.
- OutputPatternStringSuffix(String, boolean) - Constructor for class OutputPatternStringSuffix
-
Creates without a prefix.
- OutputPatternStringSuffix(String, boolean, String) - Constructor for class OutputPatternStringSuffix
-
Creates with a prefix.
- OutputPrefixerSettings - Class in org.anchoranalysis.io.output.path.prefixer
-
Arguments influencing into which directory outputs are written, and how identifiers are
expressed.
- OutputPrefixerSettings() - Constructor for class OutputPrefixerSettings
-
- OutputPrefixWithExtension - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Copies files using whatever prefix is assigned to an input by the
OutputManager as the
file-name, adding the same extension as the source file.
- OutputPrefixWithExtension() - Constructor for class OutputPrefixWithExtension
-
- outputSelectParam(CommandLine) - Static method in class SelectParamFactory
-
Can point to either:
a path ending in .xml, assumed to BeanXML for an output manager
a directory, set as the outputDirectory in the input-context
- outputsEnabled() - Method in class Outputter
-
- OutputSequence - Interface in org.anchoranalysis.io.generator.sequence
-
A sequence of elements that are written to the same directory.
- OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence
-
Creates and starts a
OutputSequence with a particular generator and context.
- OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class OutputSequenceFactory
-
- OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator, where each output increments an index by one
in the filename.
- OutputSequenceIncrementing(BoundOutputter<T>, int) - Constructor for class OutputSequenceIncrementing
-
- OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator with non-incrementing indexes for each output.
- OutputSequenceStackFactory - Class in org.anchoranalysis.image.io.stack.output
-
Creates
OutputSequence of different kinds for writing stacks to a directory.
- outputSharedObjects(SharedObjects, Optional<EnergyStack>, Outputter) - Method in class DefineOutputter
-
- OutputtedFile - Class in org.anchoranalysis.io.manifest.file
-
An entry in a
Manifest for an outputted file from an experiment.
- OutputtedFile(MutableDirectory, String, String, String, Optional<ManifestDescription>) - Constructor for class OutputtedFile
-
- OutputtedFile(MutableDirectory, String, String, String, ManifestDescription) - Constructor for class OutputtedFile
-
- Outputter - Class in org.anchoranalysis.io.output.outputter
-
- Outputter(OutputterChecked, ErrorReporter) - Constructor for class Outputter
-
- OutputterChecked - Class in org.anchoranalysis.io.output.outputter
-
A particular directory on the filesystem in which outputting can occur.
- OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define
-
Directories into which collections of different types of objects are written to in a
define experiment
- OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory
-
The directory and prefix an outputter writes to.
- OutputterTarget(DirectoryWithPrefix, boolean) - Constructor for class OutputterTarget
-
- outputToWriter(PrintWriter) - Method in class AggIDCounter
-
- outputToWriter(PrintWriter) - Method in class Aggregator
-
- OutputWriteContext - Class in org.anchoranalysis.io.output.outputter
-
Settings and user-arguments for writing files.
- OutputWriteContext() - Constructor for class OutputWriteContext
-
- OutputWriteContext(OutputWriteSettings, Optional<ImageFileFormat>) - Constructor for class OutputWriteContext
-
- OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
-
- OutputWriteFailedException(String) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(Throwable) - Constructor for exception OutputWriteFailedException
-
- OutputWriteSettings - Class in org.anchoranalysis.io.output.bean
-
Settings for how to write output, including default writers.
- OutputWriteSettings() - Constructor for class OutputWriteSettings
-
- OutsideKernelPolicy - Enum in org.anchoranalysis.image.voxel.kernel
-
How to handle voxels whose neighbours are outside ths scene.
- OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- OutsideRange() - Constructor for class OutsideRange
-
- overAll(Kernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
-
- overBox(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
-
- overBoxUntil(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class IterateKernelHelper
-
- OverlapCalculator - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Calculates overlap between object-masks
- OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapMaskBase() - Constructor for class OverlapMaskBase
-
- OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapMIPBase() - Constructor for class OverlapMIPBase
-
- OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapNumVoxels() - Constructor for class OverlapNumVoxels
-
- OverlapNumVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapNumVoxelsMask() - Constructor for class OverlapNumVoxelsMask
-
- overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class FeaturePairMemoSingleRegion
-
- overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
-
- overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class OverlapMIPBase
-
- OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label
-
An object-mask that is founded to overlap with another during labelling.
- OverlappingObject(T, ObjectMask) - Constructor for class OverlappingObject
-
- OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapRatio() - Constructor for class OverlapRatio
-
- OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapRatioMask() - Constructor for class OverlapRatioMask
-
- OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Expresses the number of intersecting pixels between two objects as a ratio to something else
(denominator)
- OverlapRelative() - Constructor for class OverlapRelative
-
- OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToFirst() - Constructor for class OverlapRelativeToFirst
-
- OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Overlap ratio to the maximum number of pixels
- OverlapRelativeToMaxVolume() - Constructor for class OverlapRelativeToMaxVolume
-
- OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToMerged() - Constructor for class OverlapRelativeToMerged
-
- OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToSecond() - Constructor for class OverlapRelativeToSecond
-
- OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
-
- overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class OverlapUtilities
-
- overlapWithGlobalMask(SessionInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
-
- overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class OverlapUtilities
-
- Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange
-
Overlays one image on the other.
- Overlay() - Constructor for class Overlay
-
- Overlay(String, String, String) - Constructor for class Overlay
-
- Overlay - Class in org.anchoranalysis.overlay
-
An entity that will eventually be drawn on top of an image.
- Overlay() - Constructor for class Overlay
-
- overlayBufferedImage(BufferedImage, BufferedImage, int, int) - Static method in class BufferedImageOverlay
-
- OverlayCollection - Class in org.anchoranalysis.overlay.collection
-
- OverlayCollection() - Constructor for class OverlayCollection
-
- OverlayCollection(Stream<Overlay>) - Constructor for class OverlayCollection
-
- OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay
-
Two-way factory.
- OverlayCollectionObjectFactory - Class in org.anchoranalysis.overlay.collection
-
Two-way factory.
- OverlayMark - Class in org.anchoranalysis.mpp.overlay
-
- OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class OverlayMark
-
- OverlayObjectMask - Class in org.anchoranalysis.overlay.object
-
- OverlayObjectMask(ObjectMask, int) - Constructor for class OverlayObjectMask
-
- OverlayProperties - Class in org.anchoranalysis.overlay
-
- OverlayProperties() - Constructor for class OverlayProperties
-
- sampleDoubleFromRange(double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range from 0
(exclusive) to endExclusive.
- sampleDoubleFromRange(double, double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range.
- sampleDoubleFromZeroCenteredRange(double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number centered around 0 ranging from
[-halfWidth,+halfWidth] (both exclusive).
- sampleDoubleZeroAndOne() - Method in interface RandomNumberGenerator
-
Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0
(exclusive).
- sampleDoubleZeroAndOne() - Method in class RandomNumberGeneratorMersenne
-
- sampleFromAvailable(int) - Method in class PartitionedMarks
-
Samples from the available marks
- sampleFromList(List<T>) - Method in interface RandomNumberGenerator
-
Samples uniformly an item from a list
- sampleInteger(int) - Method in class ProposerContext
-
Samples an integer uniformally between [0..maxVal)
- sampleIntFromRange(int) - Method in interface RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive.
- sampleIntFromRange(int, int) - Method in interface RandomNumberGenerator
-
Samples from a uniformly random discrete number within a range.
- sampleLongFromRange(long) - Method in interface RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive.
- sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollectionWithAddCriteria
-
- sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollection
-
- SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SampleWithDirectory() - Constructor for class SampleWithDirectory
-
- ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- ScalarProposer() - Constructor for class ScalarProposer
-
- ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumer but accepts three coordinates of a point as scalar arguments.
- ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumer but accepts two coordinates of a point as scalar arguments.
- scale(ScaleFactor, Interpolator, Optional<Extent>) - Method in class BoundedVoxels
-
Creates a scaled-version (in XY dimensions only) of the current bounding-box
- scale(ScaleFactor) - Method in class ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(ScaleFactor, Optional<Extent>) - Method in class ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(double) - Method in class Bound
-
- scale(double) - Method in class BoundMinMax
-
- scale(double) - Method in class ResolvedBound
-
- scale(double) - Method in class Ellipse
-
- scale(double) - Method in class Ellipsoid
-
- scale(double) - Method in class MarkWithPositionAndSingleRadius
-
Objects are scaled in pre-rotated position.
- scale(double) - Method in class Mark
-
Scales the mark in X and Y dimensions.
- scale(double) - Method in class MarkWithPosition
-
- scale(double) - Method in class LineSegment
-
- scale(double) - Method in class PointList
-
- scale(double) - Method in class Polygon
-
- scale(double) - Method in class PolygonCurve
-
- scale(Channel, ScaleCalculator, Interpolator, Optional<ImageSizeSuggestion>, MessageLogger) - Static method in class ScaleXY
-
- scale(Mask, ScaleCalculator, Optional<ImageSizeSuggestion>) - Static method in class ScaleXY
-
- Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Scales all the objects in the collection by a particular scale-factor.
- Scale() - Constructor for class Scale
-
- scale(ScaleFactor, Extent) - Method in class SegmentedObjects
-
Scales the segmented-objects.
- Scale - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- Scale() - Constructor for class Scale
-
- scale(ScaleFactor) - Method in class BoundingBox
-
Scales the bounding-box, both the corner-point and the extent
- scale(ScaleFactor, Extent) - Method in class BoundingBox
-
Scales the bounding-box corner-point, and assigns a new extent
- scale(double) - Method in class Point2d
-
- scale(double) - Method in class Point2f
-
- scale(double) - Method in class Tuple3d
-
- scale(int) - Method in class Tuple3i
-
- scale(double) - Method in class Tuple3i
-
- scale(Point2i) - Method in class ScaleFactorInt
-
Multiplies a
Point2i by the respective scaling-factor in each dimension.
- scale(Extent) - Method in class ScaleFactorInt
-
Multiplies an
Extent by the respective scaling-factor in each dimension.
- scale(ScaleFactor, Point3i) - Static method in class ScaleFactorUtilities
-
Scales a point in XY (immutably)
- ScaleableBackground - Class in org.anchoranalysis.image.io.stack.output.box
-
A stack that can be used as a background (and maybe scaled).
- scaleBy(DisplayStack, ScaleFactor, Interpolator) - Static method in class ScaleableBackground
-
Creates a background from a stack with scaling
- scaleBy(double) - Method in class Histogram
-
- ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal
- ScaleByMinMaxValue() - Constructor for class ScaleByMinMaxValue
-
- ScaleByParams - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal
- ScaleByParams() - Constructor for class ScaleByParams
-
- ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
- ScaleByTypeToByte() - Constructor for class ScaleByTypeToByte
-
- ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial
-
Calculating a scaling-factor from dimensions.
- ScaleCalculator() - Constructor for class ScaleCalculator
-
- scaleClampTo(ScaleFactor, Extent) - Method in class BoundingBox
-
Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a
containing-extent.
- ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale
-
A list of elements with an object-mask representation that have been scaled.
- scaledObjectFor(T) - Method in class ScaledElements
-
Gets the scaled version of an element given the unscaled element.
- ScaledOverlayCreator - Interface in org.anchoranalysis.overlay.object.scaled
-
Creates a scaled version of
ObjectMask to use as an overlay.
- scaleElements(List<T>, ScaleFactor, Extent, AccessObjectMask<T>) - Static method in class Scaler
-
Scales every element in a list collectively, ensuring the results remain inside a particular
region.
- ScaleFactor - Class in org.anchoranalysis.spatial.scale
-
What to scale x and y dimensions by
- ScaleFactor(double) - Constructor for class ScaleFactor
-
Create with an identical scaling-factor for all dimensions.
- ScaleFactor(double, double) - Constructor for class ScaleFactor
-
Create with specific scaling-factors for each dimension.
- ScaleFactorInt - Class in org.anchoranalysis.spatial.scale
-
Like
ScaleFactor but only allows integer scaling-factors in each dimension.
- ScaleFactorInt(int, int) - Constructor for class ScaleFactorInt
-
- ScaleFactorUtilities - Class in org.anchoranalysis.spatial.scale
-
- ScaleImage - Class in org.anchoranalysis.plugin.image.task.bean.scale
-
Creates a scaled copy of images.
- ScaleImage() - Constructor for class ScaleImage
-
- scaleObjects(ObjectCollection, ScaleFactor) - Static method in class Scaler
-
Scales every object-mask in a collection
- scaleObjects(ObjectCollection, ScaleFactor, Extent) - Static method in class Scaler
-
Scales every object-mask in a collection, ensuring the results remain inside a particular
region.
- scaleObjects(ObjectCollection, ScaleFactor, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class Scaler
-
Scales every object-mask in a collection, allowing for additional manipulation before and
after scaling.
- scaleQuantity(double, int) - Static method in class ScaleFactorUtilities
-
Multiplies a quantity (integer) by a scaling-factor, returning it as an integer
- Scaler - Class in org.anchoranalysis.image.core.object.scale
-
Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
- scaleRadii(double) - Method in class Ellipse
-
- ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
Create a thumbnail by scales an image to a particular size.
- ScaleToSize() - Constructor for class ScaleToSize
-
- scaleX(double) - Method in class Tuple3i
-
- scaleXY(double) - Method in class DualMarksAnnotation
-
Scales the marks in the annotation in X and Y dimensions.
- scaleXY(ScaleFactor) - Method in class Channel
-
- scaleXY(ScaleFactor, Interpolator) - Method in class Channel
-
- scaleXY(ScaleFactor) - Method in class Resolution
-
- scaleXY(ScaleFactor) - Method in class Mask
-
- scaleXY(double, Extent) - Method in interface Seed
-
- scaleXY(double, Extent) - Method in class SeedCollection
-
- scaleXY(double, Extent) - Method in class SeedObjectMask
-
- scaleXY(double) - Method in class MarkCollection
-
Scales the mark in X and Y dimensions.
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Scales the channel in the X and Y dimensions.
- ScaleXY() - Constructor for class ScaleXY
-
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider.resize
-
Scales the mask in XY dimensions, but not in Z dimension.
- ScaleXY() - Constructor for class ScaleXY
-
- ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- ScaleXY() - Constructor for class ScaleXY
-
- scaleXY(double) - Method in class Tuple3d
-
- scaleXY(double) - Method in class Tuple3i
-
- scaleXYBy(ScaleFactor) - Method in class Dimensions
-
- scaleXYBy(ScaleFactor) - Method in class Extent
-
- scaleXYPoint(Point3d, double) - Static method in class MarkWithPosition
-
- scaleXYTo(int, int) - Method in class Dimensions
-
- scaleY(double) - Method in class Tuple3i
-
- sceneContains(Point2i) - Static method in class CircleObjectFixture
-
- ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
- ScoreObjects() - Constructor for class ScoreObjects
-
- ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a score (a value indicating how probable something is) to each voxel
- ScoreVoxels() - Constructor for class ScoreVoxels
-
- search(FeatureCalculation<S, T>) - Method in interface CalculationResolver
-
Searches for an equivalent calculation to calculation
- search(FeatureCalculationMap<S, T, U, FeatureCalculationException>) - Method in interface CalculationResolver
-
Searches for an equivalent calculation to calculation
- SearchDirectory - Class in org.anchoranalysis.io.input.bean.files
-
Searches a directory for files whose paths match a particular predicate.
- SearchDirectory() - Constructor for class SearchDirectory
-
- Second - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Evaluates the first-object in a pair only
- Second(Feature<FeatureInputSingleObject>) - Constructor for class Second
-
- Second() - Constructor for class Second
-
- second(String) - Method in class MultiLevelBinary
-
- second(String) - Method in class MultiLevelNot
-
- second(String) - Method in interface MultiLevelOutputEnabled
-
A second-level of
OutputEnabled for a particular
outputName as used in
first-level.
- second(String) - Method in class OutputEnabledMutable
-
- second(String) - Method in class MultiLevelRecordedOutputs
-
A
RecordedOutputs for recording second-level outputs for a given
outputName
from the first-level.
- secondaryReport() - Method in class StateReporter
-
- secondaryReport() - Method in class StateReporterIdentity
-
- secondaryReport() - Method in class StateReporterToPixelized
-
- secondaryReport() - Method in class StateReporterTransformer
-
- secondEntries() - Method in class MultiLevelRecordedOutputs
-
All second-level recorded output entries.
- secondLevel(String) - Method in class RecordingWriters
-
A writer that performs a second-level check on which outputs occur, but writes to the
top-level directory.
- secondLevelOutputs(String, OutputEnabled) - Method in class OutputEnableRulesSpecify
-
- secondPart() - Method in class CombinedName
-
- secondPart() - Method in interface MultiName
-
The second part of the name.
- secondPart() - Method in class SimpleName
-
- Seed - Interface in org.anchoranalysis.image.core.object.seed
-
A seed provides an voxels that exclusively belong to a particular object, and can be used as a
starting hint for segmentation.
- SeedCollection - Class in org.anchoranalysis.image.core.object.seed
-
- SeedCollection() - Constructor for class SeedCollection
-
- SeedObjectMask - Class in org.anchoranalysis.image.core.object.seed
-
- SeedObjectMask(ObjectMask) - Constructor for class SeedObjectMask
-
- seek(int) - Method in class SlidingBuffer
-
Seeks a particular slice
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentation
-
Performs a segmentation on voxels so that each voxel has an ON or OFF state after the
operation.
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationOne
-
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationReference
-
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationThreshold
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class SegmentChannelIntoObjects
-
Segments a channel to produce an object-collection.
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class SegmentChannelIntoObjectsUnary
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary
-
- segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentIntoMarks
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class AtScale
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class ConnectedComponentsFromBinarySegmentation
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class Filter
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class ImposeMinima
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class Mser
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class WatershedYeong
-
- segment(Stack) - Method in class SegmentStackIntoObjectsPooled
-
Segments individually using a pool of size 1 just for one stack
- segment(Stack, ConcurrentModelPool<T>) - Method in class SegmentStackIntoObjectsPooled
-
Segments a stack to produce an object-collection.
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class Sequence
-
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class ThresholdAgainstChannel
-
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class FloodFillEachIntensityLevel
-
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class SegmentThresholdAboveMinBound
-
- segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentWithMarkedPointProcess
-
- segment(Stack, ConcurrentModelPool<Net>) - Method in class SegmentObjectsFromTensorFlowModel
-
- segment(Stack, ConcurrentModelPool<T>) - Method in class SuppressNonMaxima
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholder
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderMask
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderWithoutMask
-
- SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment
-
Performs some kind of segmentation
- SegmentationBean() - Constructor for class SegmentationBean
-
- SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.error
-
- SegmentationFailedException(String) - Constructor for exception SegmentationFailedException
-
- SegmentationFailedException(String, Throwable) - Constructor for exception SegmentationFailedException
-
- SegmentationFailedException(Throwable) - Constructor for exception SegmentationFailedException
-
- SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
- SegmentChannel() - Constructor for class SegmentChannel
-
- SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
- SegmentChannel() - Constructor for class SegmentChannel
-
- SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Performs segmentation of a channel using each object in the upstream collection as a mask.
- SegmentChannelByObject() - Constructor for class SegmentChannelByObject
-
- SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object
-
A base class for algorithms to segment a channel into one or more objects.
- SegmentChannelIntoObjects() - Constructor for class SegmentChannelIntoObjects
-
- SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object
-
A base-class for segmentations that takes another object-segmentation algorithm as a parameter.
- SegmentChannelIntoObjectsUnary() - Constructor for class SegmentChannelIntoObjectsUnary
-
- SegmentedObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack
-
Objects that are a result of an instance-segmentation.
- SegmentedObjects(String, Collection<WithConfidence<ObjectMask>>) - Constructor for class SegmentedObjects
-
Create for a collection of objects with an identical label.
- SegmentedObjects(Stream<LabelledWithConfidence<ObjectMask>>) - Constructor for class SegmentedObjects
-
Create for a collection of objects with potentially differing labels.
- SegmentedObjects() - Constructor for class SegmentedObjects
-
- segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class BinarySegmentationOne
-
- segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Invert
-
- segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Repeat
-
- SegmentInstanceWithModel<T> - Class in org.anchoranalysis.plugin.image.task.bean.segment
-
Using a model-pool, performs instance segmentation on an image producing zero, one or more
objects per image.
- SegmentInstanceWithModel() - Constructor for class SegmentInstanceWithModel
-
- SegmentIntoMarks - Class in org.anchoranalysis.mpp.segment.bean
-
- SegmentIntoMarks() - Constructor for class SegmentIntoMarks
-
- SegmentMarksFromImage - Class in org.anchoranalysis.plugin.mpp.experiment.bean.segment
-
Segments an image into a collection of
Marks.
- SegmentMarksFromImage() - Constructor for class SegmentMarksFromImage
-
- SegmentMarksState - Class in org.anchoranalysis.plugin.mpp.segment
-
- SegmentMarksState(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>, Define) - Constructor for class SegmentMarksState
-
- segmentMat(Mat, Dimensions, Extent, ScaleFactor, ConcurrentModelPool<Net>, Optional<List<String>>) - Method in class DecodeInstanceSegmentation
-
Performs inference, and decodes the Mat into segmented-objects.
- segmentMat(Mat, Dimensions, Extent, ScaleFactor, ConcurrentModelPool<Net>, Optional<List<String>>) - Method in class DecodeMaskRCNN
-
- segmentMat(Mat, Dimensions, Extent, ScaleFactor, ConcurrentModelPool<Net>, Optional<List<String>>) - Method in class DecodeText
-
- SegmentObjectsFromTensorFlowModel - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Performs instance-segmentation, resulting in
ObjectMasks using a TensorFlow model.
- SegmentObjectsFromTensorFlowModel() - Constructor for class SegmentObjectsFromTensorFlowModel
-
- SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D
segmentation.
- SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class SegmentOnMaximumIntensityAndExpandInZ
-
- SegmentStack<T> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Segments a stack into objects.
- SegmentStack() - Constructor for class SegmentStack
-
- SegmentStackIntoObjectsPooled<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack
-
A base class for algorithms to segment a stack into one or more objects - using a pool of models
(e.g.
- SegmentStackIntoObjectsPooled() - Constructor for class SegmentStackIntoObjectsPooled
-
- SegmentThresholdAboveMinBound - Class in org.anchoranalysis.plugin.mpp.bean.segment.binary
-
- SegmentThresholdAboveMinBound() - Constructor for class SegmentThresholdAboveMinBound
-
- SegmentWithMarkedPointProcess - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
-
Segments a channel with marked pointed processes.
- SegmentWithMarkedPointProcess() - Constructor for class SegmentWithMarkedPointProcess
-
- SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds
- SegmentWithSeeds() - Constructor for class SegmentWithSeeds
-
- select(ExecutionArguments) - Method in interface SelectParam
-
Retrieves the parameter.
- select(ExecutionArguments) - Method in class UseDefaultManager
-
- selectChannels(ChannelSource, boolean) - Method in class All
-
- selectChannels(ChannelSource, boolean) - Method in class FromStacks
-
Takes a stack-collection and extracts a set of references to particular channels (each with a
name)
- selectChannels(ChannelSource, boolean) - Method in class One
-
- selectChannels(ChannelSource, boolean) - Method in class SpecificAndRename
-
- selectDelegate(StackWriteOptions) - Method in class BranchChannels
-
- selectDelegate(StackWriteOptions) - Method in class BranchStack
-
- selectDelegate(StackWriteOptions) - Method in class BranchSuggestedFormat
-
- selectDelegate(StackWriteOptions) - Method in class StackWriterDelegateBase
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class HDF5ObjectsGenerator
-
- selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGenerator
-
Selects the file-extension to use for a particular stack.
- selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGeneratorSelectFormat
-
Combines stack-write-options derived for a particular stack with the general write-options
associated with the
RasterGenerator.
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class RGBTimeSeriesGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class DictionaryGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SerializedGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGenerator
-
Selects the file/extension to be used for outputting the file.
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGeneratorBridge
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class CSVGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class StringGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class XMLGenerator
-
- SelectFromShared<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
Selects a number of features of shared-features matching against a regular-expression
- SelectFromShared() - Constructor for class SelectFromShared
-
- selectIndexToRmv(MarkCollection, ProposerContext) - Static method in class KernelDeath
-
- selective() - Method in class RecordingWriters
-
A writer that allows only certain selected output-names, and records the written output-names
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposer
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Check
-
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposerUnary
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class MarkFromCollectionProposerUnary
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Repeat
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class UniformRandom
-
- selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class RecordedOutputsWithRules
-
- SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam
-
Different methods of selecting a object T that is used as a parameter for an experiment.
- SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam
-
Creates an appropriate
SelectParam based upon the options passed to the command-line.
- SelectSlicesBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- SelectSlicesBase() - Constructor for class SelectSlicesBase
-
- SelectSlicesWithIndexBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- SelectSlicesWithIndexBase() - Constructor for class SelectSlicesWithIndexBase
-
- separate(Collection<T>) - Method in class SpatiallySeparate
-
Splits the collection of objects into spatially separate clusters, without
consuming all elements in elements.
- separateConsume(Set<T>) - Method in class SpatiallySeparate
-
Splits the collection of objects into spatially separate clusters, consuming all
elements in elements.
- Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a sequence of succesive segmentations
- Sequence() - Constructor for class Sequence
-
- SequencedDirectory - Interface in org.anchoranalysis.io.manifest.directory.sequenced
-
- SequencedDirectoryDeserializer<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced
-
Applies a deserializer to each file in a directory with a sequence of files.
- SequencedDirectoryDeserializer(SequencedDirectory, Deserializer<T>) - Constructor for class SequencedDirectoryDeserializer
-
Creates from a manifest-directory entry.
- SequenceInteger - Class in org.anchoranalysis.bean.permute.property
-
A sequence of integers.
- SequenceInteger() - Constructor for class SequenceInteger
-
- SequenceMemory - Class in org.anchoranalysis.io.generator.sequence
-
- SequenceMemory() - Constructor for class SequenceMemory
-
- SequenceType<T> - Class in org.anchoranalysis.io.manifest.sequencetype
-
A sequence of elements (of type T), which are mapped to a range of integer indices.
- SequenceType() - Constructor for class SequenceType
-
- SequenceTypeException - Exception in org.anchoranalysis.io.manifest.sequencetype
-
- SequenceTypeException(String) - Constructor for exception SequenceTypeException
-
- SequenceTypeException(Exception) - Constructor for exception SequenceTypeException
-
- SequentialProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Executes jobs sequentially
- SequentialProcessor() - Constructor for class SequentialProcessor
-
- SequentialSession<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
Calculates features with successively different parameters, taking care of caching etc.
- SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
-
- SerializedGenerator(Optional<String>) - Constructor for class SerializedGenerator
-
- SerializedObjectSupplier<T> - Interface in org.anchoranalysis.io.manifest.finder
-
Supplies a serialized-object (if it exists)
- serializeObjectToFile(T, Path) - Static method in class XStreamSerializer
-
Writes a file with a serialized representation of an object.
- SessionInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Encapsulates a feature-input in the context of a particular session.
- SessionInputSequential<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
- SessionInputSequential(T, CacheCreator) - Constructor for class SessionInputSequential
-
Constructor
- SessionInputSequential(T, CacheCreator, ChildCacheFinder) - Constructor for class SessionInputSequential
-
- set() - Method in class StringSet
-
- set(int, double) - Method in class ResultsVector
-
- set(int, ResultsVector) - Method in class ResultsVector
-
- set(int, Seed) - Method in class SeedCollection
-
- set(int, VoxelizedMarkMemo) - Method in class MemoList
-
- set(int, UpdatableMarks) - Method in class UpdatableMarksList
-
- set(int, Mark) - Method in class MarkCollection
-
- setAboveMaxValue(double) - Method in class RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- setAcceptDirectoryErrors(boolean) - Method in class SearchDirectory
-
if true, continues when a directory-access-error occurs (logging it), otherwise throws an
exception
- setAcceptMissingResolution(boolean) - Method in class WithResolutionBase
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- setAcceptMissingResolution(boolean) - Method in class VoxelPhysicalSize
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- setAcceptNoResolution(boolean) - Method in class ReadVoxelExtentXml
-
If false, an exception is thrown if the resolution file is missing for a particular image.
- setAcceptOutsideScene(boolean) - Method in class CheckMarkWithMask
-
- setAdd(DefineAdderBean) - Method in class VisualizeOnBackground
-
- setAddCriteria(AddCriteria<T>) - Method in class RandomCollectionWithAddCriteria
-
- setAdditionalBackgrounds(List<DerivePath>) - Method in class MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- setAdditionalChannels(List<ChannelEntry>) - Method in class MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalChannels(List<ChannelEntry>) - Method in class NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalPropertyPaths(StringSet) - Method in class PermutePropertyWithPath
-
Additional property paths that are also changed, along with the main propertyPath *
- setAddName(boolean) - Method in class CombineCSV
-
- setAddOne(boolean) - Method in class Quantile
-
- setAddSum(int) - Method in class GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- setAdjacentChannels(List<AdjacentFile>) - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- setAggIntervalLog10(double) - Method in class ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- setAggregateTriggerBank(AggregateTriggerBank<T>) - Method in class FeedbackBeginParameters
-
- setAll(EnergySavedAll) - Method in class MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our
calculations for the 'all' component
- setAngleDegrees(double) - Method in class AngleRotation
-
- setAngleRadians(double) - Method in class Orientation2D
-
- setAnnealScheme(AnnealScheme) - Method in class SimulatedAnnealing
-
- setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class FromAnnotations
-
- setAnnotatorStrategy(S) - Method in class AnnotationInputManager
-
- setAppendChannels(List<AppendStack>) - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- setAppendCSV(DerivePath) - Method in class FromCSVInputManager
-
- setAppendCsv(AppendCsv) - Method in class MatchedAppendCsv
-
- setAppendDictionary(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendFilePath(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarks(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendObjects(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendStack(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setApplyResolution(boolean) - Method in class DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- setApplyToPath(boolean) - Method in class MatchRegularExpression
-
If true, the filter is applied to the path as a whole, not just the filename (using forward
slashes as directory separators)
- setArrange(ArrangeStackBean) - Method in class ArrangeRaster
-
- setArrange(ArrangeStack) - Method in class Cell
-
- setArrange(ArrangeStackBean) - Method in class CombineRasterGenerator
-
- setAsMemberFlag(byte, byte) - Static method in class RegionMembershipUtilities
-
- setAsPercentage(boolean) - Method in class Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal
- setAssigner(AnnotationComparisonAssigner<T>) - Method in class CompareAnnotations
-
- setAssignMode(AssignMode<S, T, U>) - Method in class SimulatedAnnealing
-
- setAvoidBulletOnFirst(boolean) - Method in class SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- setAvoidDivideByZero(boolean) - Method in class Divide
-
- setAvoidOverlappingObjects(boolean) - Method in class PairNeighbors
-
If true, no overlapping objects are treated as pairs
- setAxis(String) - Method in class AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- setAxis(String) - Method in class CenterOfGravity
-
- setAxis(String) - Method in class GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- setAxis(String) - Method in class ForSpecificAxis
-
- setAxis(String) - Method in class ArbitraryInsidePoint
-
- setAxis(String) - Method in class BoundingBoxAlongAxisBase
-
- setAxis(String) - Method in class GradientMeanForAxis
-
- setAxis(String) - Method in class PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- setAxis(String) - Method in class BoundingBoxExtent
-
- setAxisColor(RGBColorBean) - Method in class PlotColorScheme
-
- setAxisMax(double) - Method in class AxisLimits
-
- setAxisMin(double) - Method in class AxisLimits
-
- setBackground(AnnotationBackground) - Method in class AnnotatorStrategy
-
- setBackground(Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
-
A background image or dimensions to define an empty background.
- setBackground(ProviderAsStack) - Method in class ColoredBase
-
The background.
- setBackgroundChannelIndex(int) - Method in class OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- setBackgroundChannelName(String) - Method in class CompareAnnotations
-
- setBackgroundChannelProvider(ChannelProvider) - Method in class MorphologicalOperatorBase
-
- setBackgroundColor(RGBColorBean) - Method in class PlotColorScheme
-
- setBackgroundID(String) - Method in class VisualizeOnBackground
-
- setBackgroundStackMap(StringMap) - Method in class AnnotationBackground
-
If non-null, maps underlying stack-name to a background
- setBackgroundStackName(String) - Method in class SegmentIntoMarks
-
- setBeanExtension(String) - Method in class QuickMultiDatasetExperiment
-
- setBeanExtension(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setBelowMinValue(double) - Method in class RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- setBest(boolean) - Method in class VoxelizedMarksChangeReporter
-
- setBigNeighborhood(boolean) - Method in class Dilate
-
- setBigNeighborhood(boolean) - Method in class ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- setBigNeighborhood(boolean) - Method in class DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- setBigNeighborhood(boolean) - Method in class Dilate
-
- setBigNeighborhood(boolean) - Method in class TraverseOutlineOnImage
-
- setBinary(boolean) - Method in class ScaleImage
-
Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling
ensures only two binary-values are ouputted.
- setBinaryInputChannelID(String) - Method in class AddDistanceTransform
-
The ID of the binary input mask that determines the region of the watershed
- setBinarySgmn(BinarySegmentation) - Method in class BinarySegmentByObject
-
- setBirthRepeats(int) - Method in class KernelReplace
-
- setBit0(boolean) - Method in class RegionMembership
-
- setBit1(boolean) - Method in class RegionMembership
-
- setBit2(boolean) - Method in class RegionMembership
-
- setBit3(boolean) - Method in class RegionMembership
-
- setBit4(boolean) - Method in class RegionMembership
-
- setBit5(boolean) - Method in class RegionMembership
-
- setBit6(boolean) - Method in class RegionMembership
-
- setBit7(boolean) - Method in class RegionMembership
-
- setBitsPerPixel(int) - Method in class ForceBitsPerPixel
-
- setBlockSize(SizeXY) - Method in class HOGParameters
-
The block-size as per OpenCV implementation (identical default-size)
- setBlockStride(SizeXY) - Method in class HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size)
- setBlue(int) - Method in class RGBColorBean
-
- setBlue(int) - Method in class RGBColor
-
- setBlue(ChannelProvider) - Method in class ThreeChannels
-
- setBold(boolean) - Method in class TextStyle
-
Whether to bold the drawn text
- setBorderWidth(int) - Method in class MontageSlices
-
Adds a border around each part of the montage
- setBounds(BoundRotation) - Method in class RandomOrientation
-
- setBoundType(BoundChangeEvent.BoundType) - Method in class BoundChangeEvent
-
- setBridgeMatcher(ObjectMatcher) - Method in class Bridge
-
Used to match each input-object to an intermediary-object
- setBundleSize(int) - Method in class ObjectSerializerPeriodicReporter
-
- setBundleSize(int) - Method in class VoxelizedMarksChangeReporter
-
- setBySlices(boolean) - Method in class ConnectedComponentsFromMask
-
- setCacheSize(int) - Method in class RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- setCalculateLevel(CalculateLevel) - Method in class CalculateLevelOne
-
- setCalculateLevel(CalculateLevel) - Method in class ThresholderGlobal
-
- setCalculateLevel(CalculateLevel) - Method in class LevelPerObjectBase
-
Method to calculate the level for a particular object.
- setCalculateLevel(CalculateLevel) - Method in class GreaterThanThreshold
-
Calculates the level for the threshold
- setCalculateLevel(CalculateLevel) - Method in class LevelFromHistogram
-
- setCalculateLevel(CalculateLevel) - Method in class ThresholdHistogram
-
- setCalculateLevel(CalculateLevel) - Method in class CalculateLevelBase
-
- setCalculateLevelElse(CalculateLevel) - Method in class CalculateLevelRelativeToThreshold
-
- setCaseSensitive(boolean) - Method in class PatternSpan
-
Iff true, a case sensitive search is used to match patterns.
- setCellDefault(ArrangeStackBean) - Method in class Tile
-
- setCells(List<Cell>) - Method in class Tile
-
- setCellSize(SizeXY) - Method in class HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size)
- setCenterPoint(Point3d) - Method in class FitResult
-
- setChangeExisting(boolean) - Method in class ConvertBase
-
If true, the existing channel can be changed.
- setChannel(ChannelProvider) - Method in class ChannelProviderUnary
-
- setChannel(ChannelProvider) - Method in class ChannelFilter
-
- setChannel(ChannelProvider) - Method in class FromChannel
-
- setChannel(ChannelProvider) - Method in class FromChannel
-
- setChannel(ChannelProvider) - Method in class FromChannelBase
-
- setChannel(ChannelProvider) - Method in class IntensityGreaterEqualThan
-
- setChannel(ChannelProvider) - Method in class UnaryWithChannelBase
-
- setChannel(ChannelProvider) - Method in class WithChannelBase
-
- setChannel(ChannelProvider) - Method in class FromChannelOrMask
-
A channel that is provided to the stack.
- setChannel1(ChannelProvider) - Method in class ChannelProviderBinary
-
- setChannel1(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannel2(ChannelProvider) - Method in class ChannelProviderBinary
-
- setChannel2(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannel3(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannelAssignFrom(ChannelProvider) - Method in class AssignFromChannel
-
- setChannelConversionStyle(ChannelConvertStyle) - Method in class ConvertImageFormat
-
To convert as RGB or independently or in another way
- setChannelConverter(ConvertChannelTo<T>) - Method in class Convert
-
- setChannelConverter(ConvertChannelTo<?>) - Method in class ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
- setChannelElse(ChannelProvider) - Method in class IfParamEquals
-
- setChannelFilter(ChannelFilter) - Method in class ConvertImageFormat
-
Optionally, includes only certain channels when converting.
- setChannelFirst(int) - Method in class Difference
-
Index of first channel
- setChannelGroupID(int) - Method in class RegularExpression
-
- setChannelID(String) - Method in class AddEdgeFilters
-
The ID of the channel that provides the input to the filter
- setChannelIfVoxelZero(ChannelProvider) - Method in class IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
- setChannelIndex(int) - Method in class FromStack
-
- setChannelIndex(int) - Method in class FromStackChannel
-
- setChannelIndex(int) - Method in class One
-
- setChannelIndex(int) - Method in class MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which
channel to use from the stack
- setChannelLookup(ChannelProvider) - Method in class NormalizeDifferenceToMedian
-
- setChannelMap(ChannelMap) - Method in class NamedChannels
-
- setChannelMask(String) - Method in class ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the
histogram
- setChannelName(String) - Method in class ChannelFilter
-
- setChannelName(String) - Method in class SingleChannel
-
- setChannelName(String) - Method in class ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- setChannelSecond(int) - Method in class Difference
-
Index of second channel
- setChannelsExtra(List<ChannelProvider>) - Method in class ScoreVoxels
-
- setChannelsPerByteArray(int) - Method in class ForceChannelsPerByteArray
-
- setChannelThreshold(ChannelProvider) - Method in class ThresholdAgainstChannel
-
- setCheck(CheckMark) - Method in class Not
-
- setCheckMark(CheckMark) - Method in class FromObjects
-
- setCheckMark(CheckMark) - Method in class Check
-
- setCheckMark(CheckMark) - Method in class Check
-
- setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class GroupFiles
-
Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be
included.
- setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class BinaryClassifierImageLabeller
-
- setClassLabelsPath(String) - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the class-labels file, a text file where each line specifies a class label in order, relative to the models/ directory in the Anchor distribution.
- setClearOutsideMask(boolean) - Method in class ThresholdAgainstChannel
-
- setCol(int) - Method in class Cell
-
- setCollapseFilename(boolean) - Method in class FilePathAppendBase
-
- setCollectionID(String) - Method in class ParamFromCollection
-
- setColor(RGBColorBean) - Method in class FromSingle
-
The single color to repeat.
- setColor(RGBColorBean) - Method in class AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- setColor(RGBColorBean) - Method in class ColoredMask
-
- setColors(ColorScheme) - Method in class ColorSchemeUnary
-
The delegate that creates the (unshuffled) list.
- setColors(List<RGBColorBean>) - Method in class FromList
-
The list of colors to specify
- setColors(ColorScheme) - Method in class ColoredBaseWithGenerator
-
Colors to use for drawing objects
- setColorScheme(ColorScheme) - Method in class GenerateToMatchObjects
-
- setColorsUnpaired(ColorScheme) - Method in class CompareAnnotations
-
- setColorUnselectedObjects(RGBColorBean) - Method in class OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- setColumnDefinition(ColumnDefinition) - Method in class ExportObjectsFromCSV
-
Column definition for the CSV files
- setColumnGroup(String) - Method in class ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- setColumnID(String) - Method in class ColumnDefinition
-
Name of CSV column with the file identifier
- setColumns(int) - Method in class MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- setColumnUniquePixel(String) - Method in class ColumnDefinition
-
Name of CSV column with X coordinate of point for the first Object
- setCombine(CombineObjectsForFeatures<T>) - Method in class FromObjects
-
- setCommand(String) - Method in class MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- setComparerLeft(Comparer) - Method in class AnnotationComparisonInputManager
-
- setComparerRight(Comparer) - Method in class AnnotationComparisonInputManager
-
- setCondition(DictionaryCondition) - Method in class IfParamEquals
-
- setCondition(DictionaryCondition) - Method in class IfKeyValueCondition
-
- setConfidenceThreshold(double) - Method in class ConditionallyMergeOverlappingObjects
-
The maximum difference in confidence for merging.
- setConstant(double) - Method in class MaxWithConstant
-
- setContains(String) - Method in class DescriptiveNameContainsImageLabeller
-
- setContains(String) - Method in class FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- setConvert(ConvertChannelToWithHistogram<T>) - Method in class ConvertWithHistogram
-
- setConvexHull(boolean) - Method in class FitPointsFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- setCopyFilesNaming(CopyFilesNaming<NoSharedState>) - Method in class CopyFilesNamingOne
-
- setCountThreshold(int) - Method in class SummarizerSplitMoreThan
-
If there are more than countThreshold elements, use summarizerGreaterThan,
else summarizerElse.
- setCov(boolean) - Method in class ObjectRadiusStandardDeviation
-
- setCreateMark(CreateMarkFromPoints) - Method in class PointsFitter
-
- setCreateShort(boolean) - Method in class ArrangeRaster
-
- setCreateShort(boolean) - Method in class GenerateString
-
- setCreateShort(boolean) - Method in class TileWithLabels
-
- setCreateShort(boolean) - Method in class DistanceTransform3D
-
- setCreateShort(boolean) - Method in class DistanceTransformForEachObject3D
-
- setCreateShort(boolean) - Method in class CreateNew
-
If True creates an unsigned short-image
- setCsvFilePath(DerivePath) - Method in class FilterCsvColumn
-
- setCsvIgnoreZeros(boolean) - Method in class ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- setCurrentTemp(double) - Method in class Geometry
-
- setCustomName(String) - Method in class Feature
-
An optional additional name that be associated with the feature (defaults to an empty string)
- setDatasetName(String) - Method in class ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- setDatasetNameSubdirectory(boolean) - Method in class ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- setDatasets(StringSet) - Method in class QuickMultiDatasetExperiment
-
- setDatasets(StringSet) - Method in class QuickMultiDatasetStructuredExperiment
-
- setDatasetSpecific(String) - Method in class QuickMultiDatasetExperiment
-
- setDatasetSpecific(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setDatasetSuffix(String) - Method in class FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- setDatasetVersion(String) - Method in class ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- setDay(boolean) - Method in class ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output
- setDebug(boolean) - Method in class RootPath
-
If true this root is preferred, when executing a job in debugging mode
- setDebug(boolean) - Method in class ThresholdedFeature
-
- setDebugModeParams(Optional<DebugModeParams>) - Method in class InputContextParams
-
Parameters for debug-mode (only defined if we are in debug mode)
- setDecode(DecodeInstanceSegmentation) - Method in class SegmentObjectsFromTensorFlowModel
-
Decodes inference output into segmented objects.
- setDefaultBehaviourString(Optional<String>) - Method in class ExperimentExecutor
-
If present, a string is printed in the description if the default-experiment is used,
otherwise ignored.
- setDefaultColors(ColorScheme) - Method in class OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- setDefine(Define) - Method in class MarkEvaluator
-
- setDefine(Define) - Method in class DefineOutputter
-
- setDefine(DefineOutputter) - Method in class Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- setDefine(DefineOutputter) - Method in class ExportReportFeaturesFromMulti
-
- setDefine(DefineOutputterWithEnergy) - Method in class FromObjects
-
- setDefine(DefineOutputter) - Method in class ExportObjectsAsCroppedImages
-
- setDefine(DefineOutputterWithEnergy) - Method in class SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- setDelaySizeAtEnd(int) - Method in class MovieFromSlices
-
- setDelegate(ResolvedBound) - Method in class BoundMinMax
-
- setDelimiter(String) - Method in class DirectoryWithPrefix
-
Added between prefix and the filename, if the filename is defined.
- setDelimiter(String) - Method in class SubsetRangeIfRequested
-
Character used to split the name into groups.
- setDelimiter(String) - Method in class LastDirectoryAsPrefix
-
- setDelta(double) - Method in class Mser
-
- setDeltat(double) - Method in class AnisotropicDiffusion
-
- setDepth(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in z-dimension.
- setDerivePath(DerivePath) - Method in class AnnotationMarksComparer
-
- setDerivePath(DerivePath) - Method in class MarksComparer
-
- setDerivePath(DerivePath) - Method in class MaskComparer
-
- setDerivePath(DerivePath) - Method in class ObjectComparer
-
- setDerivePath(DerivePath) - Method in class CollapseFileName
-
- setDerivePath(DerivePath) - Method in class RemoveTrailingDirectory
-
- setDictionary(DictionaryProvider) - Method in class ParametersAsFeatures
-
- setDictionary(Dictionary) - Method in class EnergyStack
-
- setDictionary(DictionaryProvider) - Method in class FeatureEvaluator
-
Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
- setDictionary(DictionaryProvider) - Method in class EnergySchemeCreatorByElement
-
- setDictionary(DictionaryProvider) - Method in class ScaleByParams
-
- setDictionary(DictionaryProvider) - Method in class AssignFromDictionary
-
The dictionary from which an assignment will occur.
- setDictionary(DictionaryProvider) - Method in class ScoreVoxels
-
- setDictionary(DictionaryProvider) - Method in class IfParamEqual
-
- setDictionary(DictionaryProvider) - Method in class DictionaryCondition
-
The dictionary to provide a value to check.
- setDictionary(DictionaryProvider) - Method in class FeatureListProviderLDAClassifier
-
- setDictionary(DictionaryProvider) - Method in class FeatureValueCheckMark
-
- setDictionary(DictionaryProvider) - Method in class DefineOutputterWithEnergy
-
- setDictionary(DictionaryProvider) - Method in class GaussianSampler
-
The dictionary that parameterizes the Gaussian-distribution that is sampled from.
- setDictionary(String) - Method in class Develop
-
If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
- setDictionary(DictionaryProvider) - Method in class SegmentMarksFromImage
-
If non-empty, the identifier of a key-value-params collection that is passed to the
segmentation procedure.
- setDimensions(DimensionsProvider) - Method in class ReportFeatureForMarks
-
- setDimensions(DimensionsProvider) - Method in class FromDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class FromDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class RepeatSlice
-
Dimensions to create new mask
- setDimensions(DimensionsProvider) - Method in class MergeBase
-
- setDimensions(DimensionsProvider) - Method in class WithDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class WithOptionalDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class ToDimensions
-
The dimensions the source image/entity is desired to be scaled to.
- setDimensions(DimensionsProvider) - Method in class FromMarks
-
- setDimensions(DimensionsProvider) - Method in class RequireFeatureRelationThreshold
-
- setDimensions(DimensionsProvider) - Method in class PointsFitterToMark
-
- setDimensionsSourceFallback(DimensionsProvider) - Method in class ToDimensions
-
- setDirection(DirectionVectorBean) - Method in class ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- setDirection(VectorInDirection) - Method in class FeatureMarkDirection
-
- setDirectionVector(VectorInDirection) - Method in class FromUnitValueDistance
-
- setDirectory(String) - Method in class FilesProviderWithDirectoryString
-
A directory in which to look for files.
- setDirectory(Path) - Method in class DirectoryWithPrefix
-
- setDirectory(String) - Method in class HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- setDirectoryDataset(String) - Method in class QuickMultiDatasetExperiment
-
- setDirectoryDistance(int) - Method in class QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- setDirectoryOutput(String) - Method in class QuickExperiment
-
- setDisableDebugMode(boolean) - Method in class RootedFilePath
-
- setDisableDebugMode(boolean) - Method in class Rooted
-
- setDisablePathModification(boolean) - Method in class MarkAnnotationWriter
-
- setDistance(int) - Method in class LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching
neighbors, distance==2 implies those touching the directly touching etc.)
- setDistanceMapProvider(ChannelProvider) - Method in class MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- setDistanceMax(double) - Method in class CalculateLevel
-
- setDistanceTransformMultiplyBy(float) - Method in class AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short
- setDistanceTransformSmoothSigmaMeters(double) - Method in class AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters
below
- setDistanceX(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceY(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceZ(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceZEndIfEmpty(UnitValueDistance) - Method in class XYOrientationExtendToZ
-
- setDivideByZeroValue(double) - Method in class Divide
-
- setDivisor(double) - Method in class PermutePropertySequenceDouble
-
Divide by
- setDivisor(int) - Method in class IdentifierModulo
-
What the identifier is divided by to find the modulo.
- setDo3D(boolean) - Method in class AnisotropicDiffusion
-
- setDo3D(boolean) - Method in class ObjectCollectionProviderMorphological
-
- setDo3D(boolean) - Method in class MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- setDo3D(boolean) - Method in class PairNeighbors
-
- setDo3D(boolean) - Method in class TouchingVoxels
-
- setDo3D(boolean) - Method in class Erode
-
- setDo3D(boolean) - Method in class NumberRemovedVoxelsAfterClosing
-
- setDo3D(boolean) - Method in class OutlineKernelBase
-
- setDo3D(boolean) - Method in class UniformRandomRadiiProposer
-
- setDrawReverseLine(boolean) - Method in class Orientation
-
- setDuplicate(boolean) - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data
This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setDuplicate(boolean) - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting
data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class EnergySchemeCreatorByElement
-
- setElement(T) - Method in class LabelledWithConfidence
-
- setElement(T) - Method in class WithConfidence
-
- setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class EnergySchemeCreatorByElement
-
- setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class EnergySchemeCreatorByElement
-
- setEmptyValue(double) - Method in class CenterOfGravity
-
- setEmptyValue(double) - Method in class Intersection
-
- setEmptyValue(double) - Method in class ArbitraryInsidePoint
-
- setEmptyValue(int) - Method in class IntensityMeanMaxSlice
-
- setEmptyValue(double) - Method in class IntensityMeanShellBase
-
- setEmptyValue(double) - Method in class DerivedObject
-
- setEnd(int) - Method in class SequenceInteger
-
An index beyond which we cannot iterate (inclusive)
- setEnd(int) - Method in class IncrementingIntegers
-
- setEnergyChannelIndex(int) - Method in class Identity
-
- setEnergyChannelIndex(int) - Method in class RejectIfIntensityLessThan
-
- setEnergyChannelIndex(int) - Method in class SingleChannel
-
- setEnergyChannelIndex(int) - Method in class QuantileAcrossConnectedComponents
-
- setEnergyChannelIndexCheck(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setEnergyChannelIndexFail(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setEnergyIndex(int) - Method in class NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- setEnergyIndex(int) - Method in class OutsideRange
-
- setEnergyIndex(int) - Method in class Intensity
-
The channel that that forms the histogram
- setEnergyIndex(int) - Method in class AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's
dimensions
- setEnergyIndex(int) - Method in class OverlapMaskBase
-
- setEnergyIndexGradient(int) - Method in class TextureScore
-
- setEnergyIndexMask(int) - Method in class IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for
ON and OFF
- setEnergyIndexMask(int) - Method in class Intensity
-
Optionally, index of another channel that masks the histogram.
- setEnergyIndexX(int) - Method in class IntensityGradientBase
-
- setEnergyIndexY(int) - Method in class IntensityGradientBase
-
- setEnergyIndexZ(int) - Method in class IntensityGradientBase
-
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class MarkEvaluator
-
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- setEnergyStack(EnergyStack) - Method in class FeatureInputEnergy
-
- setEnergyStack(Optional<EnergyStack>) - Method in class FeatureInputEnergy
-
- setEnergyTotal(double) - Method in class MarksWithTotalEnergy
-
The pre-annealed total energy
- setEnergyTotal(double) - Method in class EnergySavedInd
-
- setEquals(String) - Method in class FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- setErodeAtBoundary(boolean) - Method in class ConvexHullBase
-
- setError(int, Exception) - Method in class ResultsVector
-
- setErrorAll(Exception) - Method in class ResultsVector
-
- setErrorDisconnectedObjects(boolean) - Method in class RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- setErrorTree(DefaultTreeModel) - Method in class ProposerFailureDescription
-
- setExactDepth(int) - Method in class DirectoryDepth
-
- setExceptionIfEmpty(boolean) - Method in class FeatureHistogramStatistic
-
If true, then an exception is thrown if the histogram is empty, otherwise
is returned.
- setExcludeZero(boolean) - Method in class Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- setExcludeZero(boolean) - Method in class IntensityMeanMaxSlice
-
- setExcludeZero(boolean) - Method in class Intensity
-
If true, zeros are excluded from considering in the histogram
- setExecutionTime(long) - Method in class OptimizationStep
-
- setExitBeforeOptimization(boolean) - Method in class SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- setExitWithMinima(boolean) - Method in class WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- setExpandLabelZ(boolean) - Method in class TileWithLabels
-
- setExperiment(RootedExperiment) - Method in class ExperimentResultsExperimentStructure
-
- setExperiment(RootedExperiment) - Method in class ExperimentStructure
-
- setExperimentIdentifier(ExperimentIdentifier) - Method in class OutputExperiment
-
A name for the experiment.
- setExperimentType(String) - Method in class FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same
directory
- setExperimentType(String) - Method in class QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- setExperimentType(String) - Method in class RootedExperiment
-
A directory identifying the type of experiment.
- setExpression(String) - Method in class RegExSimple
-
A Java-style regular expression containing groups.
- setExpression(String) - Method in class MatchRegularExpression
-
- setExpression(String) - Method in class RegularExpression
-
- setExtendInZ(boolean) - Method in class ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
- setExtension(String) - Method in class OneOrThreeChannelsWriter
-
- setExtension(String) - Method in class AppendStack
-
- setExtension(String) - Method in class AppendStackDirect
-
- setExtensions(Set<String>) - Method in class MatchExtensions
-
A set of file-extensions (without the period), one of which must match the end of a path.
- setExtensions(StringSet) - Method in class BranchExtension
-
Any extensions to match (case insensitive) not including any leading period.
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class DirectAssignMode
-
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class UniformProposal
-
- setExtractScoreSizeReport(ExtractScoreSize<S>) - Method in class TransformationAssignMode
-
- setExtractScoreSizeState(ExtractScoreSize<T>) - Method in class TransformationAssignMode
-
- setExtractWeight(ExtractWeightFromMark) - Method in class KernelInitialMarksFromPartition
-
- setExtraLength(int) - Method in class Midpoint
-
- setFactor(double) - Method in class ScoreObjects
-
- setFactor(double) - Method in class Scale
-
- setFactorHigh(double) - Method in class Identity
-
- setFactorLow(double) - Method in class Identity
-
- setFactorStandardDeviation(double) - Method in class GaussianSampler
-
Multiples the standard deviation of the distribution found in keyStandardDeviation.
- setFallback(FilesProvider) - Method in class SpecificPathList
-
If no paths can be found either from listPaths or the input-context, then the fallback is
called if exists, otherwise an error is thrown
- setFallback(ScaleCalculator) - Method in class ToSuggested
-
- setFallback(ChannelConvertStyle) - Method in class RGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- setFallbackName(String) - Method in class ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name
- setFeature(FeatureListElem<T>) - Method in class ListSequence
-
The list feature that is duplicated, and populated.
- setFeature(Feature<T>) - Method in class FeatureProviderDefine
-
- setFeature(Feature<T>) - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session.
- setFeature(FeatureListEvaluator<FeatureInputSingleObject>) - Method in class OutputFeatureTable
-
A list of features to calculate in an evaluation context.
- setFeature(Feature<FeatureInputSingleObject>) - Method in class ScoreObjects
-
Feature that calculates the score for an object.
- setFeature(Feature<T>) - Method in class PermuteFeatureBase
-
- setFeature(Feature<FeatureInputPairMemo>) - Method in class AddCriteriaFeatureRelationThreshold
-
- setFeature(FeatureProvider<T>) - Method in class FeatureValueCheckMark
-
- setFeature(FeatureProvider<FeatureInputMark>) - Method in class RequireFeatureRelationThreshold
-
- setFeatureCondition(Feature<T>) - Method in class IfCondition
-
- setFeatureCondition(Feature<T>) - Method in class IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- setFeatureElse(Feature<T>) - Method in class IfCondition
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MultipleComparer
-
- setFeatureEvaluator(FeatureEvaluator<T>) - Method in class ReportFeatureEvaluator
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class FeatureCostAssigner
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class DiscardOutliers
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ThresholdedFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ObjectCollectionProviderWithFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeGreedyToIncreaseObjectFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeToIncreaseObjectFeature
-
- setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches
-
- setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MergePairs
-
- setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- setFeatureListRef(String) - Method in class FeatureProviderReference
-
- setFeatureProvider(FeatureProvider<T>) - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- setFeatures(List<FeatureProvider<T>>) - Method in class FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a
session
- setFeatures(List<NamedBean<FeatureListProvider<U>>>) - Method in class ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation)
- setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class ExportFeatures
-
Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
- setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every
object.
- setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- setFeatureTables(List<OutputFeatureTable>) - Method in class Develop
-
Specifies a feature-table that can also be outputted.
- setFeedbackReceiver(FeedbackReceiverBean<T>) - Method in class FeedbackReceiverRequireArguments
-
- setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy>) - Method in class SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- setFileFilter(String) - Method in class ExperimentResultsExperimentStructure
-
Files to search for
- setFileFilterAndDirectory(Path) - Method in class SearchDirectory
-
Sets both the fileFilter and the Directory from a combinedFileFilter string
- setFileId(String) - Method in class AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- setFileId(String) - Method in class FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- setFileInput(NamedFiles) - Method in class GroupFiles
-
- setFileInput(InputManager<FileInput>) - Method in class NamedChannels
-
- setFileInput(InputManager<FileInput>) - Method in class Stacks
-
- setFileInput(String) - Method in class QuickExperiment
-
A string indicating the input file(s)
- setFileName(String) - Method in class ReportFeatureForManifestFileBase
-
- setFilePath(String) - Method in class SortedSetSlice
-
- setFilePath(String) - Method in class FromSerializedMarks
-
- setFilePath(String) - Method in class FromSerializedObject
-
- setFilePathParser(FilePathParser) - Method in class MultiFileReader
-
- setFilePathProviderSVM(FilePathProvider) - Method in class FeatureListProviderSVMClassifier
-
- setFilePrefix(String) - Method in class MovieFromSlices
-
- setFiles(FilesProvider) - Method in class ReadFromFile
-
Provides a single file containing a dictionary.
- setFiles(FilesProvider) - Method in class FilesProviderUnary
-
- setFiles(FilesProviderWithDirectory) - Method in class FilesProviderWithDirectoryUnary
-
- setFiles(FilesProvider) - Method in class FromFiles
-
A provider that should return exactly one
File whose path is employed.
- setFiles(FilesProviderWithDirectory) - Method in class Rooted
-
- setFiles(FilesProvider) - Method in class NamedFiles
-
The files to use as inputs.
- setFiles(FilesProviderWithDirectory) - Method in class NamedFilesWithDirectory
-
The files to use as inputs.
- setFiles(FilesProviderWithDirectory) - Method in class QuickBase
-
A path to the main channel of each file
- setFilter(ObjectFilter) - Method in class IfObjectFilter
-
- setFilter(ObjectFilter) - Method in class ObjectCollectionProviderFilterBase
-
- setFilter(ObjectFilter) - Method in class Filter
-
- setFilter(ImageLabeller<T>) - Method in class ImageLabellerStringMap
-
- setFilterFilesCsv(MatchedAppendCsv) - Method in class QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- setFindMaxima(boolean) - Method in class ExtractSlice
-
If true, the maxima of the score is searched for.
- setFindOutlinePixelAngle(FindPointOnOutline) - Method in class TraversePointsOnContour
-
- setFirst(StringSet) - Method in class OutputEnableRulesSpecify
-
Output-names in the first-level.
- setFirst(boolean) - Method in class AsSingle
-
Iff true, first object is used, otherwise the second
- setFirst(StateTransformerBean<S, U>) - Method in class Compose
-
First transformation from S to U
- setFirstLineHeaders(boolean) - Method in class CombineCSV
-
- setFixRandomSeed(boolean) - Method in class SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- setFlatten(boolean) - Method in class Outline
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make
it 2D
- setFlatten(boolean) - Method in class ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity
projection), so that a 2D image is produced
- setFontColor(RGBColorBean) - Method in class TextStyle
-
Font-color of drawn text
- setFontName(String) - Method in class TextStyle
-
Font-name of drawn text
- setFontSize(int) - Method in class TextStyle
-
Font-size of drawn text
- setForceChangeBytes(boolean) - Method in class Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer
to reflect the existing binary-values.
- setForceDetailedLogging(boolean) - Method in class OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- setForceEagerEvaluation(boolean) - Method in class NamedChannelsAppend
-
- setForceReader(String) - Method in class BioformatsReader
-
If non-empty forces usage of a particular bioformats plugin
- setForceRGB(boolean) - Method in class ArrangeRaster
-
If set, ensures every stack is converted into 3 channels
- setForwardDirectionOnly(boolean) - Method in class XYOrientationExtendToZ
-
- setFrom3i(ObjectMask) - Static method in class PointsFromObject
-
A sorted-set of three-dimensional integer points from the entire object-mask
- setFromOutline(ObjectMask) - Static method in class PointsFromObject
-
- setGaussian(boolean) - Method in class AddEdgeFilters
-
If true, the Gaussian filter is included
- setGaussianSigmaMeters(double) - Method in class AddEdgeFilters
-
- setGeneratorList(List<RasterGenerator<T>>) - Method in class CombineRasterGenerator
-
- setGlob(String) - Method in class MatchGlob
-
The string describing a glob e.g.
- setGradient(ChannelProvider) - Method in class ScoreVoxels
-
- setGraphColorScheme(PlotColorScheme) - Method in class PlotIndexBase
-
- setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class MinimaImpositionGrayscaleReconstruction
-
- setGreen(int) - Method in class RGBColorBean
-
- setGreen(int) - Method in class RGBColor
-
- setGreen(ChannelProvider) - Method in class ThreeChannels
-
- setGroup(String) - Method in class AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- setGroup(DerivePath) - Method in class ExportFeatures
-
If non-null this file-path is used to determine the group of the file If null, no group is
included.
- setGroup(DerivePath) - Method in class GroupedStackBase
-
If defined, translates a file-path into a group.
- setGroup(String) - Method in class CSVRow
-
- setGroup(String) - Method in class AppendHistogram
-
- setGroupNum(int) - Method in class RootFilePathRegEx
-
- setHeight(int) - Method in class SizeXY
-
Size in Y dimension.
- setHeight(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in y-dimension.
- setHighestTwoRadiiOnly(boolean) - Method in class RadiiRatio
-
- setHistogram(HistogramProvider) - Method in class HistogramProviderUnary
-
- setHistogram(HistogramProvider) - Method in class ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple
images).
- setHistogram(HistogramProvider) - Method in class SegmentChannel
-
An optional histogram of voxel intensity values which can be used by segment
- setHistogram(HistogramProvider) - Method in class PlotHistogram
-
The histogram to plot.
- setHistogram(HistogramProvider) - Method in class FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the
inputted CSV.
- setHistogramChannelIndex(int) - Method in class CalculateLevelBase
-
- setHistogramIndex(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setHistogramsExtra(List<HistogramProvider>) - Method in class ScoreVoxels
-
- setHorizontalAlign(String) - Method in class Overlay
-
- setId(String) - Method in class DictionaryProviderReference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class FeatureProviderReference
-
- setId(String) - Method in class StatisticForFeature
-
- setId(String) - Method in class BinarySegmentationReference
-
- setId(String) - Method in class FilePathProviderReference
-
- setId(int) - Method in class Mark
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class FromChannel
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class ReferenceOrElse
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class FeatureIntersectingObjects
-
ID for the particular object-collection
- setId(DerivePath) - Method in class ExportFeatures
-
Translates an input file name to a unique ID
- setId(String) - Method in class MarkBoundsReference
-
- setId(String) - Method in class MarkProposerReference
-
- setId(String) - Method in class MarkMergeProposerReference
-
- setId(String) - Method in class MarkSplitProposerReference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class ReferenceOrEmpty
-
- setId(int) - Method in class CreateEllipse
-
- setId(String) - Method in class CSVRow
-
- setId(String) - Method in class Reference
-
- setIdentifierSubrange(Optional<IndexRange>) - Method in class InputContextParams
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- setIdentifierSuffix(String) - Method in class QuickMultiDatasetExperiment
-
- setIdentifierSuffix(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setIdGenerator(DerivePath) - Method in class ExportObjectsFromCSV
-
- setIdGetter(IdentifierGetter<T>) - Method in class IdentifierModulo
-
- setIgnoreAtThreshold(boolean) - Method in class OutlineKernelBase
-
- setIgnoreCase(boolean) - Method in class FilePathPattern
-
if true, case is ignored in the pattern matching.
- setIgnoreContains(String) - Method in class AnnotationBackground
-
If non-empty any stackNames (after map) containing a certain string will be ignored
- setIgnoreFileNotFoundAppend(boolean) - Method in class NamedChannelsAppend
-
- setIgnoreFittingFailure(boolean) - Method in class FitPointsFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply
not included (with only a log error) If false, an exception is thrown
- setIgnoreHidden(boolean) - Method in class SearchDirectory
-
if true, case is ignored in the pattern matching.
- setIgnoreHidden(boolean) - Method in class FilePathPattern
-
Iff true, any hidden-path is not considered, and simply ignored
- setIgnoreHigherSide(boolean) - Method in class GaussianCumulative
-
- setIgnoreLowerSide(boolean) - Method in class GaussianCumulative
-
- setIgnoreMissingChannel(boolean) - Method in class IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- setIgnoreNaN(boolean) - Method in class Sum
-
If true, we ignore any NaN values.
- setIgnoreNoObjects(boolean) - Method in class SegmentInstanceWithModel
-
If true, then the outputs (outline, mask, image etc.) are not written for images that produce
no objects.
- setIgnoreRangeAxisOutside(boolean) - Method in class LinePlot
-
- setIgnoreZero(boolean) - Method in class RatioNonMode
-
- setIgnoreZeros(boolean) - Method in class HistogramCSVGenerator
-
Iff true bins in the histogram with a zero count are not written
- setIgnoreZIfNaN(boolean) - Method in class DistanceTransform3D
-
If the z-resolution is undefined, the z dimenion is ignored.
- setImageLabeller(ImageLabeller<T>) - Method in class ImageAssignLabel
-
Maps a label to an image
- setImgChannelMapCreator(ChannelMap) - Method in class GroupFiles
-
- setIncludeDirectories(boolean) - Method in class DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- setIncludeFeatureNames(boolean) - Method in class EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the
actual features
- setIncludeFileName(boolean) - Method in class AppendDictionary
-
- setIncludeFirst(boolean) - Method in class PairNeighbors
-
Include features for the First-object of the pair
- setIncludeMerged(boolean) - Method in class PairNeighbors
-
Include features for the Merged-object of the pair
- setIncludeSecond(boolean) - Method in class PairNeighbors
-
Include features for the Second-object of the pair
- setIncludeShell(boolean) - Method in class MaxOverlapRatio
-
- setIncludeZ(boolean) - Method in class Outline
-
If true the outline is also applied in the z-dimension, otherwise this is ignored as possible
boundary
- setIncludeZ(boolean) - Method in class NotTouchingSceneBorder
-
- setIncrement(int) - Method in class SequenceInteger
-
Size of step to use when incrementing
- setIndex(int) - Method in interface IndexSetter
-
- setIndex(int, double) - Method in class DirectionVector
-
Sets an element of the vector by the index of its position, index=0 is the X-element, index=1
is the Y-element etc.
- setIndex(int) - Method in class ChannelEntry
-
- setIndex(int) - Method in class KernelPointCursor
-
- setIndex(int) - Method in class AtIndex
-
- setIndex(int) - Method in class SliceAt
-
Index in z-dimension of slice to extract
- setIndex(int) - Method in class SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue,
1=second-largest eigenvalue etc.)
- setIndex(int) - Method in class IndexedRegionBase
-
- setIndex(int) - Method in class OrderedRadius
-
- setIndex(int) - Method in class AsObject
-
- setIndex(int) - Method in class HOGFeature
-
Which index to return from the HOG descriptor
- setIndexEnd(int) - Method in class ExtractSliceRange
-
Slice index to end extracting from (inclusive).
- setIndexNonZero(int) - Method in class SelectSlicesWithIndexBase
-
- setIndexStart(int) - Method in class ExtractSliceRange
-
Slice index to start extracting from (inclusive).
- setInitContext(OptimizationContext) - Method in class FeedbackBeginParameters
-
- setInitialKernel(Kernel<T, S>) - Method in class KernelProposer
-
- setInnerCoreDistance(double) - Method in class Ellipsoid
-
- setInput(InputManager<T>) - Method in class AnnotationInputManager
-
- setInput(InputManager<T>) - Method in class InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- setInput(InputManager<T>) - Method in class InputManagerUnary
-
- setInput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setInput(InputManager<? extends ProvidesStackInput>) - Method in class MultiInputManager
-
- setInput(InputManager<T>) - Method in class AnnotationComparisonInputManager
-
- setInput(InputManager<NamedChannelsInputPart>) - Method in class NamedChannelsAppend
-
- setInput(InputManager<T>) - Method in class Exclude
-
- setInput(InputManager<NamedChannelsInput>) - Method in class ConvertNamedChannelsToStack
-
- setInput(MultiInputManager) - Method in class FromCSVInputManager
-
- setInputDebug(InputManager<T>) - Method in class BranchIfDebug
-
- setInputDirectory(Optional<Path>) - Method in class InputContextParams
-
If defined, a directory which can be used by beans to find input.
- setInputFilterExtensions(Set<String>) - Method in class InputContextParams
-
A list of extensions that can be used filter inputs
- setInputFilterGlob(String) - Method in class InputContextParams
-
A glob that can be used by beans to filter input
- setInputName(String) - Method in class MultiInputManager
-
- setInputName(String) - Method in class QuickExperiment
-
- setInputName(String) - Method in class MultiInputManagerQuick
-
- setInputPaths(Optional<List<Path>>) - Method in class InputContextParams
-
A list of paths referring to specific inputs
- setInputPointShift(float) - Method in class ConicFitterBase
-
- setIntensity(ChannelProvider) - Method in class ScoreVoxels
-
- setIntensityProvider(Provider<Stack>) - Method in class GenerateString
-
- setInterpolate(boolean) - Method in class AtScale
-
- setInterpolator(InterpolatorBean) - Method in class ScaleXY
-
- setInterpolator(InterpolatorBean) - Method in class OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- setInterpolator(InterpolatorBean) - Method in class ScaleToSize
-
- setInverse(boolean) - Method in class IntersectsWithContainer
-
- setInverse(boolean) - Method in class IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is
removed)
- setInverseMask(boolean) - Method in class IntensityMeanShellBase
-
- setInvert(boolean) - Method in class MaskComparer
-
- setInvert(boolean) - Method in class FromObjects
-
- setInvert(boolean) - Method in class FilterWithRegularExpression
-
Iff true, then a file is rejected if the regular-expression matches and vice-versa.
- setInvertDecisionValue(boolean) - Method in class FeatureListProviderSVMClassifier
-
- setItem(T) - Method in class NamedBean
-
The item that is to be named (i.e.
- setItem(T, int) - Method in class SingleContainer
-
- setItem(Feature<T>) - Method in class DefineSingle
-
- setItem(FeatureListProvider<FeatureInput>) - Method in class PrependName
-
- setItem(Feature<S>) - Method in class FeatureUnary
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureDeriveFromPair
-
- setItem(ReportFeature<MarksInitialization>) - Method in class ReportFeatureWrapError
-
- setItem(Feature<FeatureInputHistogram>) - Method in class ThresholdHistogram
-
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class DeriveFromPair
-
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding "aggregate" feature is created in the output
list
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleObject>) - Method in class DerivedObject
-
- setItem(Feature<FeatureInputPairObjects>) - Method in class FeatureIntersectingObjectsSingleElement
-
- setItem(FeaturePairObjects) - Method in class PairedWithMask
-
- setItem(VoxelScore) - Method in class RejectIfIntensityLessThan
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
-
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleObject>) - Method in class AsObjectMask
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class QuantileAcrossConnectedComponents
-
- setItem(DerivePath) - Method in class Rooted
-
- setItem(Feature<FeatureInputSingleMemo>) - Method in class CoefficientOfVarianceFromAll
-
- setItem(Feature<FeatureInputSingleMemo>) - Method in class MeanFromAll
-
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleMemo>) - Method in class FeaturePairMemoOne
-
- setItem1(Feature<T>) - Method in class FeatureDoubleElem
-
- setItem2(Feature<T>) - Method in class FeatureDoubleElem
-
- setItemMean(Feature<T>) - Method in class StatisticalBase
-
- setItemProportionate(Feature<FeatureInputSingleMemo>) - Method in class FeatureAsIndividualProportionate
-
- setItemStdDev(Feature<T>) - Method in class StatisticalBase
-
- setIterations(int) - Method in class AnisotropicDiffusion
-
- setIterations(int) - Method in class MorphologicalOperatorBase
-
- setIterations(int) - Method in class ObjectCollectionProviderMorphological
-
- setIterations(int) - Method in class Repeat
-
The maximum number of iterations.
- setIterations(MorphologicalIterations) - Method in class Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- setIterations(MorphologicalIterations) - Method in class IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- setIterations(int) - Method in class Erode
-
- setIterations(int) - Method in class NumberRemovedVoxelsAfterClosing
-
- setIterations(MorphologicalIterations) - Method in class Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- setIterations(int) - Method in class MorphologicalOperation
-
iterations for erode, dilate, open, close
- setIterations(int) - Method in class UniformProposal
-
- setIterations(int) - Method in class NumberIterationsBase
-
The number of iterations for which the number-of-marks must remain constant.
- setIterationsDilation(int) - Method in class MorphologicalIterations
-
Number of times to perform morphological dilation
- setIterationsErosion(int) - Method in class MorphologicalIterations
-
Number of times to perform morphological erosion
- setJobNumber(int) - Method in class JobDescription
-
- setJobShortName(String) - Method in class JobDescription
-
- setKappa(double) - Method in class AnisotropicDiffusion
-
- setKeepEntireImage(boolean) - Method in class ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
- setKeepExtremes(boolean) - Method in class Identity
-
- setKeepProcessorsFree(int) - Method in class DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- setKeepProcessorsFree(int) - Method in class ParallelProcessor
-
How many processors to avoid using for the tasks.
- setKeepZ(boolean) - Method in class ImposeResolution
-
Keep the z-resolution if it is already defined
- setKernel(Kernel<T, S>) - Method in class WeightedKernel
-
- setKernel(Kernel<T, S>) - Method in class KernelProposerOptionSingle
-
- setKernelFactoryList(WeightedKernelList<?, ?>) - Method in class FeedbackBeginParameters
-
- setKernelHalfWidth(int) - Method in class Median
-
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
- setKernelNegative(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual
-
- setKernelPositive(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual
-
- setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- setKernelStateBridge(KernelStateBridge<U, T>) - Method in class TransformationAssignMode
-
- setKey(String) - Method in class AssignFromDictionary
-
The key of the value in the dictionary that will be assigned.
- setKey(String) - Method in class IfParamEqual
-
- setKey(String) - Method in class DictionaryCondition
-
The key in the dictionary whose value is checked.
- setKey(String) - Method in class ParamFromCollection
-
- setKey(String) - Method in class FromDictionary
-
- setKeyGroupID(int) - Method in class RegularExpression
-
- setKeyLower(String) - Method in class ScaleByParams
-
- setKeyMean(String) - Method in class GaussianSampler
-
The name of the key in the dictionary with the mean of the distribution.
- setKeyPrefix(String) - Method in class FromDictionary
-
Prefix prepended to key
- setKeyRequired(boolean) - Method in class RegularExpression
-
- setKeyStandardDeviation(String) - Method in class GaussianSampler
-
The name of the key in the dictionary with the standard-deviation.
- setKeySuffix(String) - Method in class FromDictionary
-
- setKeyUpper(String) - Method in class ScaleByParams
-
- setLabel(String) - Method in class StackProviderWithLabel
-
- setLabel(boolean) - Method in class MontageSlices
-
If true a label is added beside every image showing the slice index
- setLabels(List<AnnotationLabel>) - Method in class WholeImageLabelStrategy
-
- setLevel(int) - Method in class Constant
-
- setLine(String[]) - Method in class CSVRow
-
- setList(List<DefineAdderBean>) - Method in class Concatenate
-
- setList(List<RegEx>) - Method in class RegExList
-
- setList(List<StringMapItem>) - Method in class StringMap
-
- setList(List<LoggingDestination>) - Method in class ToMultiple
-
The list of loggers to log to
- setList(List<Feature<T>>) - Method in class Define
-
- setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class DefinedNamed
-
- setList(List<Feature<T>>) - Method in class FeatureList
-
- setList(List<Feature<T>>) - Method in class FeatureListElem
-
- setList(FeatureList<T>) - Method in class FeatureListElem
-
- setList(List<Provider<Stack>>) - Method in class ArrangeRaster
-
- setList(List<DrawObject>) - Method in class Combine
-
- setList(List<StackProviderWithLabel>) - Method in class TileWithLabels
-
- setList(List<RegionMembership>) - Method in class RegionMap
-
- setList(List<AddCriteriaPair>) - Method in class AddCriteriaOr
-
- setList(List<FeedbackReceiver<T>>) - Method in class FeedbackReceiverList
-
- setList(List<TerminationCondition>) - Method in class TerminationConditionListOr
-
- setList(List<ColorProvider>) - Method in class Concatenate
-
- setList(List<CalculateLevel>) - Method in class CalculateLevelListBase
-
- setList(List<ObjectFilter>) - Method in class ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- setList(List<ObjectCollectionProvider>) - Method in class Concatenate
-
- setList(List<BinarySegmentation>) - Method in class Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor
becomes the input of the sucecssor)
- setList(List<ProviderAsStack>) - Method in class Concatenate
-
- setList(List<NamedBean<FromStack>>) - Method in class SpecificAndRename
-
- setList(List<ChannelEntry>) - Method in class FromEntries
-
- setList(List<FilesProvider>) - Method in class Combine
-
- setList(List<InputManager<T>>) - Method in class Concatenate
-
- setList(List<Summarizer<T>>) - Method in class SummarizerAggregate
-
- setList(List<CheckMark>) - Method in class AndList
-
- setList(List<VisitScheduler>) - Method in class VisitSchedulerAnd
-
- setList(List<VisitScheduler>) - Method in class VisitSchedulerUniformSample
-
- setList(List<MarkProposer>) - Method in class MarkProposerFromList
-
- setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class ScoreObjects
-
- setListAppend(List<NamedBean<DerivePath>>) - Method in class NamedChannelsAppend
-
- setListAppend(List<FilePathBaseAppendToManager>) - Method in class MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- setListComparers(List<NamedBean<Comparer>>) - Method in class MultipleComparer
-
- setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class BinaryClassifierImageLabeller
-
- setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class EnergySchemeCreatorByElement
-
- setListPaths(List<String>) - Method in class SpecificPathList
-
If specified, this forms the list of paths which is provided as input.
- setListReportFeatures(List<ReportFeature<U>>) - Method in class ExportReportFeatures
-
- setListStackProvider(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setListStackProviderMIP(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setLocalized(boolean) - Method in class FilesProviderWithDirectoryString
-
- setLog(LoggingDestination) - Method in class OnlyIf
-
The logger to use if conditions are fulfilled
- setLogExperiment(LoggingDestination) - Method in class OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- setLogExperimentPath(String) - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- setLoggerTaskCreator(LoggingDestination) - Method in class ParametersExperiment
-
This is a means to create new log-reporters for each task.
- setLogPath(boolean) - Method in class Rooted
-
if true, the pathIn and pathOut are logged.
- setLogTask(LoggingDestination) - Method in class InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- setLogTaskPath(String) - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- setMainChannelIndex(int) - Method in class NamedChannelsQuick
-
Index of the mainChannel
- setMainChannelName(String) - Method in class NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- setManifestDescriptionFunction(String) - Method in class MarksGeneratorBase
-
- setManifestDeserializer(ManifestDeserializer) - Method in class CoupledManifestsInputManager
-
- setManifestExperimentInputFileSet(FilesProvider) - Method in class CoupledManifestsInputManager
-
- setManifestFunction(String) - Method in class ObjectSerializerPeriodicReporter
-
- setManifestFunction(String) - Method in class VoxelizedMarksChangeReporter
-
- setManifestInputFileSet(FilesProvider) - Method in class CoupledManifestsInputManager
-
- setMap(StringMap) - Method in class ImageLabellerStringMap
-
- setMarkBounds(MarkBounds) - Method in class MarkBoundsDefine
-
- setMarkBounds(MarkBounds) - Method in class SegmentThresholdAboveMinBound
-
- setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- setMarkFactory(MarkWithIdentifierFactory) - Method in class MarkEvaluator
-
- setMarkFactory(MarkWithIdentifierFactory) - Method in class SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- setMarkFactory(MarkFactory) - Method in class FitPointsFromObjects
-
- setMarkFromMarksProposer(MarkFromCollectionProposer) - Method in class KernelSplit
-
- setMarkProposer(String) - Method in class MarkProposerStrategy
-
- setMarkProposer(MarkProposer) - Method in class FromMarkProposer
-
- setMarkProposer(MarkProposer) - Method in class MergeMarkEllipse
-
- setMarkProposer(MarkProposer) - Method in class MarkEllipseSimple
-
- setMarkProposer(MarkProposer) - Method in class KernelBirthAndKill
-
- setMarkProposer(MarkProposer) - Method in class KernelExchange
-
- setMarkProposer(MarkProposer) - Method in class KernelBirthPixelized
-
- setMarkProposerAdditionalBirth(MarkProposer) - Method in class KernelBirthAndKill
-
- setMarkProvider(SingleMarkProvider) - Method in class CreateMarkFromPoints
-
- setMarkProvider(SingleMarkProvider) - Method in class ReportFeatureOnMark
-
- setMarkProvider(SingleMarkProvider) - Method in class FromSingleMark
-
- setMarkProvider(Provider<Optional<Mark>>) - Method in class RequireFeatureRelationThreshold
-
- setMarks(MarkCollection) - Method in class MarksWithTotalEnergy
-
The marks
- setMarks(MarkCollectionProvider) - Method in class ReportFeatureOnMarks
-
- setMarks(MarkCollection) - Method in class MarksWithDisplayStack
-
- setMarks(Point2d, Orientation) - Method in class Ellipse
-
- setMarks(MarkCollectionProvider) - Method in class FromMarks
-
- setMarks(MarkCollectionProvider) - Method in class ScaleXY
-
- setMarks(MarkCollectionProvider) - Method in class RetrieveSingleMarkOnly
-
- setMarks(MarkCollectionProvider) - Method in class ColoredMarks
-
- setMarksColored(ColoredMarks) - Method in class ColoredMarksWithDisplayStack
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class ConicBase
-
- setMarksExplicit(Point3d, Orientation) - Method in class ConicBase
-
- setMarksExplicit(Point3d) - Method in class ConicBase
-
- setMarksExplicit(Point3d, Orientation, Point2d) - Method in class Ellipse
-
- setMarksExplicit(Point3d) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipsoid
-
- setMarksExplicit(Point3d) - Method in class Ellipsoid
-
- setMarksExplicit(Point3d, Orientation) - Method in class Ellipsoid
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksFromPartition
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksProposed
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksVoxelized
-
- setMask(Provider<Mask>) - Method in class MaskProviderUnary
-
- setMask(MaskProvider) - Method in class FromMaskBase
-
- setMask(MaskProvider) - Method in class UnaryWithMaskBase
-
- setMask(MaskProvider) - Method in class ScoreVoxels
-
- setMask(MaskProvider) - Method in class FromChannel
-
- setMask(MaskProvider) - Method in class SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask
has an ON voxel
- setMask(Provider<Mask>) - Method in class ConnectedComponentsFromMask
-
- setMask(MaskProvider) - Method in class AndObjectsWithMasks
-
- setMask(Provider<Mask>) - Method in class FromMask
-
- setMask(MaskProvider) - Method in class SegmentChannel
-
- setMask(MaskProvider) - Method in class ColoredMask
-
- setMask(Provider<Mask>) - Method in class FromChannelOrMask
-
A mask that is provided to the stack.
- setMask(MaskProvider) - Method in class PairedWithMask
-
- setMask(MaskProvider) - Method in class MaskAsSingleObject
-
- setMask(MaskProvider) - Method in class FillHoles
-
- setMask(Provider<Mask>) - Method in class CheckMarkWithMask
-
- setMask(Provider<Mask>) - Method in class FindPointOnOutlineWalk
-
- setMask(Provider<Mask>) - Method in class XYOrientationExtendToZ
-
- setMaskElse(MaskProvider) - Method in class IfPredicateBase
-
Returned instead of mask if the predicate is not satisfied
- setMaskFilled(Provider<Mask>) - Method in class TraverseOutlineOnImage
-
- setMaskFilled(Provider<Mask>) - Method in class XYOrientationExtendToZ
-
- setMaskIndex(int) - Method in class SurfaceSizeMaskNonZero
-
- setMaskOutline(Provider<Mask>) - Method in class TraverseOutlineOnImage
-
- setMaskValue(int) - Method in class ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- setMaskValue(int) - Method in class OverlapMaskBase
-
- setMatch(RegEx) - Method in class SelectFromShared
-
- setMatch(String) - Method in class FilterCsvColumn
-
- setMatch(String) - Method in class MatchedAppendCsv
-
- setMatcher(PathMatcher) - Method in class SearchDirectory
-
- setMatcher(PathMatcher) - Method in class MatchExtensions
-
- setMatcher(ObjectMatcher) - Method in class RelationWithMatches
-
- setMatcher(ObjectMatcher) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- setMatcher(ObjectMatcher) - Method in class Match
-
- setMax(int) - Method in interface Progress
-
- setMax(int) - Method in class ProgressConsole
-
- setMax(int) - Method in class ProgressIgnore
-
- setMax(int) - Method in class ProgressIncrement
-
- setMax(int) - Method in class ProgressOneOfMany
-
- setMax(double) - Method in class BoundMinMax
-
- setMax(double) - Method in class ResolvedBound
-
- setMax(int) - Method in class ScaleByMinMaxValue
-
- setMax(int) - Method in class ClampHistogramMax
-
- setMax(UnitValueAreaOrVolume) - Method in class UnitsWithinRange
-
Maximum-boundary for acceptable range
- setMax(boolean) - Method in class IdentityImposeValueRelationToHistogram
-
- setMax(int) - Method in class OutsideRange
-
- setMax(double) - Method in class MaxOverlapRatio
-
- setMax(double) - Method in class InvertedMax
-
- setMax(Feature<T>) - Method in class CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- setMax(double) - Method in class RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- setMaxCost(double) - Method in class MultipleComparer
-
- setMaxCost(double) - Method in class FeatureCostAssigner
-
- setMaxDirectoryDepth(int) - Method in class SearchDirectory
-
If non-negative the max depth of directories.
- setMaxDirectoryDepth(int) - Method in class ExperimentResultsExperimentStructure
-
- setMaxDistance(UnitValueDistance) - Method in class MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- setMaxDistance(UnitValueDistance) - Method in class CostOverlapWithinMidpointDistance
-
- setMaxDistance(UnitValueDistance) - Method in class FindPointOnOutlineWalk
-
- setMaxDistanceBetweenMinima(UnitValueDistance) - Method in class AddDistanceTransform
-
- setMaxDistanceCOG(UnitValueDistance) - Method in class MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- setMaxDistanceDeltaContour(double) - Method in class AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- setMaxDistanceDeltaContour(double) - Method in class MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the
distanceMap for each point.
- setMaxDistanceProposer(ScalarProposer) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- setMaxDistanceZ(ScalarProposer) - Method in class XYOrientationExtendToZ
-
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class RadiiProposerRepeat
-
- setMaxNumberItems(int) - Method in class Limit
-
- setMaxNumberItems(int) - Method in class Limit
-
- setMaxNumberProcessors(int) - Method in class DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- setMaxNumberProcessors(int) - Method in class ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- setMaxNumberProcessors(int) - Method in class QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- setMaxNumberProcessors(int) - Method in class QuickMultiDatasetStructuredExperiment
-
- setMaxNumItems(int) - Method in class LimitWithDirectory
-
- setMaxScaleFactor(int) - Method in class LargestMultipleWithin
-
An upper limit on the scale-factor allowed in each dimension.
- setMaxSize(long) - Method in class Mser
-
- setMaxSplitGroups(int) - Method in class CompareAnnotations
-
- setMaxValue(long) - Method in class ToByteScaleByMaxValue
-
- setMaxVar(double) - Method in class Mser
-
- setMaxVolume(UnitValueAreaOrVolume) - Method in class FillHoles
-
- setMaxX(int) - Method in class InsideBoxOn
-
Maximum X coordinate inclusive
- setMaxY(int) - Method in class InsideBoxOn
-
Maximum Y coordinate inclusive
- setMaxZ(int) - Method in class InsideBoxOn
-
Maximum Z coordinate inclusive
- setMean(double) - Method in class FirstSecondOrderStatistic
-
Mean
- setMedian(boolean) - Method in class AddEdgeFilters
-
If true, the median filter is included
- setMedianRadiusMeters(double) - Method in class AddEdgeFilters
-
- setMerge(boolean) - Method in class CutBelowThreshold
-
- setMergedPosTolerance(double) - Method in class MergeMarkEllipse
-
- setMergeMarkProposer(MarkMergeProposer) - Method in class KernelMerge
-
- setMessage(String) - Method in class ReportFeatureWrapError
-
- setMessageNoInputs(String) - Method in class InputOutputExperiment
-
A message written to the logger if no inputs exist for the experiment, and it thus ends
early.
- setMethod(String) - Method in class AutoLocalThreshold
-
- setMethod(String) - Method in class ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string
for the default).
- setMethod(CopyFilesMethod) - Method in class CopyFiles
-
How the copying occurs from source to destination file.
- setMin(int) - Method in interface Progress
-
- setMin(int) - Method in class ProgressConsole
-
- setMin(int) - Method in class ProgressIgnore
-
- setMin(int) - Method in class ProgressIncrement
-
- setMin(int) - Method in class ProgressOneOfMany
-
- setMin(double) - Method in class BoundMinMax
-
- setMin(double) - Method in class ResolvedBound
-
- setMin(int) - Method in class ScaleByMinMaxValue
-
- setMin(UnitValueAreaOrVolume) - Method in class UnitsWithinRange
-
Minimum-boundary for acceptable range
- setMin(int) - Method in class OutsideRange
-
- setMin(double) - Method in class RadiiMinRatio
-
- setMin(Feature<T>) - Method in class CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- setMin(double) - Method in class RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- setMinConfidence(double) - Method in class ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be included.
- setMinConfidence(float) - Method in class DecodeMaskRCNN
-
Only proposals outputted from the model with a score greater or equal to this threshold are
considered.
- setMinConfidence(double) - Method in class DecodeText
-
Proposed bounding boxes below this confidence interval are removed
- setMinDiff(double) - Method in class MeanIntensityDifference
-
- setMinDifference(int) - Method in class Difference
-
A minimum difference, below which 0.0 is returned
- setMinDifference(int) - Method in class DifferenceCalculateLevelStandardDeviation
-
- setMinDiversity(double) - Method in class Mser
-
- setMinimaImposition(MinimaImposition) - Method in class ImposeMinima
-
- setMinimumBoundingBoxVolume(int) - Method in class FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- setMinimumSize(SizeXY) - Method in class LargestMultipleWithin
-
The minimum size in each dimension.
- setMinIntensity(int) - Method in class RejectIfIntensityLessThan
-
- setMinIntensity(int) - Method in class ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- setMinIntensityValue(int) - Method in class MorphologicalOperatorBase
-
- setMinMaskValue(float) - Method in class DecodeMaskRCNN
-
Threshold above which pixels are considered in the mask.
- setMinMaxIgnoreBeforeIndex(int) - Method in class LinePlot
-
- setMinMaxValues(int, int) - Method in class ToByteScaleByMinMaxValue
-
- setMinNumberObjects(int) - Method in class DiscardOutliers
-
- setMinNumberPoints(int) - Method in class SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- setMinNumberVoxels(int) - Method in class SplitIntoSquares
-
Only includes squares that have at least this number of voxels.
- setMinNumberVoxels(int) - Method in class ConnectedComponentsFromBinarySegmentation
-
- setMinNumberVoxels(int) - Method in class ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- setMinNumPoints(int) - Method in class CreateMarkFromPoints
-
- setMinNumPoints(int) - Method in class PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- setMinNumSlices(int) - Method in class XYOrientationExtendToZ
-
- setMinNumZSlices(int) - Method in class AtLeastZSlices
-
- setMinOverlap(double) - Method in class CostOverlapWithinMidpointDistance
-
- setMinRadius(double) - Method in class LinearLeastSquaresEllipseFitter
-
- setMinRadius(double) - Method in class LinearLeastSquaresEllipsoidFitter
-
- setMinRadScaleEnd(double) - Method in class MarkEllipseSimple
-
- setMinRadScaleStart(double) - Method in class MarkEllipseSimple
-
- setMinRatio(double) - Method in class DiscardOutliers
-
- setMinResolution(double) - Method in class MinimumXYResolution
-
- setMinSize(long) - Method in class Mser
-
- setMinVal(double) - Method in class FeatureValueCheckMark
-
- setMinVolume(UnitValueAreaOrVolume) - Method in class ConnectedComponentsFromMask
-
- setMinVolume(UnitValueVolume) - Method in class VolumeMin
-
- setMinVolumeConnectedComponent(UnitValueVolume) - Method in class AddDistanceTransform
-
- setMinX(int) - Method in class InsideBoxOn
-
Minimum X coordinate inclusive
- setMinY(int) - Method in class InsideBoxOn
-
Minimum Y coordinate inclusive
- setMinZ(int) - Method in class InsideBoxOn
-
Minimum Z coordinate inclusive
- setMip(boolean) - Method in class NumberVoxels
-
- setMip(boolean) - Method in class SurfaceNumberVoxelsBase
-
- setMip(boolean) - Method in class OverlapMIPBase
-
- setModelBinaryPath(String) - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb extension, relative to the models/ directory in the Anchor distribution.
- setModelTextGraphPath(String) - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb.txt extension, relative to the models/ directory in the Anchor distribution.
- setMultipleComparer(MultipleComparer) - Method in class MarkProposerStrategy
-
- setMultiplyBy(float) - Method in class DistanceTransform3D
-
- setName(String) - Method in class FromXmlList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- setName(String) - Method in class NamedBean
-
The name associated with item
- setName(S, String) - Method in interface ApplyPermutations.NameSetter
-
- setName(String) - Method in class RootPath
-
- setName(String) - Method in interface NameValue
-
Sets the associated namme
- setName(String) - Method in class SimpleNameValue
-
- setName(String) - Method in class ExperimentIdentifierConstant
-
- setName(String) - Method in class ChannelEntry
-
- setName(String) - Method in class Kernel
-
- setName(String) - Method in class WeightedKernel
-
- setName(String) - Method in class AdjacentFile
-
A name to describe the adjacent file
- setName(String) - Method in class FilePathAppendBase
-
The name of the appended entity
- setNameLeft(String) - Method in class AnnotationComparisonInputManager
-
- setNamer(FileNamer) - Method in class GroupFiles
-
- setNamer(FileNamer) - Method in class RemoveExtension
-
- setNamer(FileNamer) - Method in class SubsetRangeIfRequested
-
The namer that is called to provide names that are subsetted.
- setNamer(FileNamer) - Method in class NamedFilesBase
-
- setNamer(FileNamer) - Method in class QuickBase
-
Assigns each input a unique compact name.
- setNameRight(String) - Method in class AnnotationComparisonInputManager
-
- setNaming(CopyFilesNaming<T>) - Method in class CopyFiles
-
How an output name (and path) is selected for an input file.
- setNavigateHigherDirs(int) - Method in class MultiFileReader
-
Search x number directories higher than file
- setNewNameOnFeature(Feature<? extends FeatureInput>, String, String) - Static method in class PrependName
-
- setNoBlack(boolean) - Method in class ThresholderAutoIJ
-
- setNormalize(boolean) - Method in class Identity
-
- setNormalize(boolean) - Method in class BoundingBoxZOverlapRatio
-
- setNormalizeFeatures(boolean) - Method in class FeatureListProviderSVMClassifier
-
Normalize features
- setNumberBins(int) - Method in class HOGParameters
-
The number of bins in each histogram for a cell
- setNumberChannels(int) - Method in class ForceNumberChannels
-
- setNumberColors(int) - Method in class TiffTimeSeries
-
- setNumberColumns(int) - Method in class Tile
-
The number of columns to use in the table produced when tiling.
- setNumberColumns(int) - Method in class CSVReader.OpenedCSVFile
-
- setNumberDecimalPlaces(int) - Method in class FeatureCostAssigner
-
- setNumberDigits(int) - Method in class IncrementingNumber
-
Number of digits in the number, with leading zeros as necessary.
- setNumberDilations(int) - Method in class LevelPerObjectIndependently
-
- setNumberFrames(int) - Method in class ForceNumberFrames
-
- setNumberGPUProcessors(int) - Method in class ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- setNumberLevelsGrouping(int) - Method in class CompareAnnotations
-
- setNumberLoopPoints(int) - Method in class SplitContourAtSaddlePoints
-
- setNumberPoints(int) - Method in class LinePlot
-
- setNumberRows(int) - Method in class Tile
-
The number of rows to use in the table produced when tiling.
- setNumberSubdirectories(int) - Method in class LastDirectories
-
How many directories to include in the name.
- setNumCols(int) - Method in class TileWithLabels
-
- setNumMarks(int) - Method in class FromMarkProposer
-
- setObjectMatcher(ObjectMatcher) - Method in class Bridge
-
Used to match each intermediary-object to a final-object
- setObjects(Provider<ObjectCollection>) - Method in class ObjectCollectionProviderUnary
-
- setObjects(ObjectCollectionProvider) - Method in class OutputFeatureTable
-
The objects for which features are calculated.
- setObjects(ObjectCollectionProvider) - Method in class ReportFeatureOnObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class DistanceTransformForEachObject3D
-
- setObjects(ObjectCollectionProvider) - Method in class LevelPerObjectBase
-
The objects for whom a level is calculated
- setObjects(ObjectCollectionProvider) - Method in class UnaryWithObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class GenerateToMatchObjects
-
- setObjects(ObjectCollectionProvider) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class IntersectsWith
-
- setObjects(ObjectCollectionProvider) - Method in class Always
-
- setObjects(ObjectCollectionProvider) - Method in class Intersection
-
- setObjects(ObjectCollectionProvider) - Method in class Permute
-
- setObjects(ObjectCollectionProvider) - Method in class ColoredObjects
-
Objects to draw on a background
- setObjects(ObjectCollectionProvider) - Method in class ObjectAggregationBase
-
- setObjects(ObjectCollectionProvider) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class ObjectAsPoints
-
- setObjects(ObjectCollectionProvider) - Method in class IncludeRandomObjects
-
- setObjects(ObjectCollectionProvider) - Method in class PointsFromObjects
-
- setObjects(List<NamedBean<ObjectCollectionProvider>>) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class ExportObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class PointsFitterToMark
-
- setObjects1(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise
-
First collection with items to be merged
- setObjects2(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- setObjectsBlue(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsContainer(ObjectCollectionProvider) - Method in class WithContainerBase
-
- setObjectsElse(ObjectCollectionProvider) - Method in class ReferenceOrElse
-
- setObjectsGreater(ObjectCollectionProvider) - Method in class GreaterIntersectionWith
-
- setObjectsGreen(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsGrouped(ObjectCollectionProvider) - Method in class FilterByGroup
-
- setObjectsLesser(ObjectCollectionProvider) - Method in class GreaterIntersectionWith
-
- setObjectsRed(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsRejected(ObjectCollectionProvider) - Method in class ObjectCollectionProviderFilterBase
-
- setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentChannel
-
- setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentWithSeeds
-
- setObjectsSource(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects
-
- setObjectsSource(ObjectCollectionProvider) - Method in class SegmentWithSeeds
-
- setObjectsSplitBy(ObjectCollectionProvider) - Method in class SplitByObjects
-
- setObjectsTarget(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects
-
- setOfConnectedComponentIDs() - Method in class EncodedVoxels
-
- setOff(int, int, int) - Method in interface BinaryOnOffSetter
-
- setOff(Point3i) - Method in interface BinaryOnOffSetter
-
- setOn(int, int, int) - Method in interface BinaryOnOffSetter
-
- setOn(Point3i) - Method in interface BinaryOnOffSetter
-
- SetOperationFailedException - Exception in org.anchoranalysis.core.index
-
- SetOperationFailedException(String) - Constructor for exception SetOperationFailedException
-
- SetOperationFailedException(Throwable) - Constructor for exception SetOperationFailedException
-
- setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
- setOptionList(List<KernelProposerOption<T, S>>) - Method in class KernelProposer
-
- setOptions(ReadOptions) - Method in class BioformatsReader
-
Options that influence how stack is read.
- setOptions(ReadOptions) - Method in class ReadOptionsDelegate
-
- setOrientationProposer(OrientationProposer) - Method in class OrientationAndRadiiProposer
-
- setOrientationXYProposer(OrientationProposer) - Method in class XYOrientationExtendToZ
-
- setOtherwise(FileNamer) - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is not selected.
- setOutline(boolean) - Method in class ColoredBase
-
If true, an outline is drawn around the entries.
- setOutlineAtBoundary(boolean) - Method in class Outline
-
- setOutlineColor(RGBColorBean) - Method in class SegmentInstanceWithModel
-
The color of the outline
- setOutlinePixelsRetriever(OutlinePixelsRetriever) - Method in class TraversePointsOnContour
-
- setOutlinePixelsRetrieverReverse(OutlinePixelsRetriever) - Method in class TraversePointsOnContour
-
- setOutlineWidth(int) - Method in class BoundingBoxOutline
-
- setOutlineWidth(int) - Method in class Outline
-
- setOutlineWidth(int) - Method in class CompareAnnotations
-
- setOutlineWidth(int) - Method in class AtScale
-
- setOutlineWidth(int) - Method in class ColoredBase
-
The width of the outline (only relevant if outline==true
- setOutlineWidth(int) - Method in class OutlinePreserveRelativeSize
-
The width of the outline.
- setOutlineWidth(int) - Method in class SegmentInstanceWithModel
-
The width of the outline
- setOutlineWidth(int) - Method in class VisualizeOnBackground
-
- setOutlineWidth(int) - Method in class ExportObjectsAsCroppedImages
-
- setOutPath(String) - Method in class InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- setOutput(OutputManager) - Method in class OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- setOutput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setOutput(String) - Method in class QuickMultiDatasetExperiment
-
- setOutputName(String) - Method in class ToTextFileBase
-
The name to use (without extension) for the text-file log
- setOutputName(String) - Method in class OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- setOutputName(String) - Method in class PeriodicSubdirectoryReporter
-
- setOutputName(String) - Method in class MinimalExecutionTimeStatsReporter
-
- setOutputName(String) - Method in class VoxelizedMarksChangeReporter
-
- setOutputNameStyle(IndexableOutputNameStyle) - Method in class FromOutputName
-
- setOutputRGBOutline(StringSet) - Method in class ExportObjectsAsCroppedImages
-
- setOutputRGBOutlineFlattened(StringSet) - Method in class ExportObjectsAsCroppedImages
-
- setOutputsDisabled(StringSet) - Method in class SpecificDisabled
-
The names of the outputs that are disbled.
- setOutputsEnabled(StringSet) - Method in class SpecificEnabled
-
The names of the outputs that are enabled.
- setOutputsEnabled(OutputEnabledRules) - Method in class OutputManager
-
Which outputs are enabled or not enabled.
- setOutputShort(boolean) - Method in class GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- setOutputStackProvider(StackProvider) - Method in class ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the
groupIdentifier.
- setOutputWriteSettings(OutputWriteSettings) - Method in class OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- setOutputWriteSettings(OutputWriteSettings) - Method in class QuickExperiment
-
- setOutside(double) - Method in class UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- setOutsideAtThreshold(boolean) - Method in class OutlineKernelBase
-
- setOverlapRatioThreshold(double) - Method in class KernelBirthAndKill
-
- setOverlapThreshold(double) - Method in class ConditionallyMergeOverlappingObjects
-
The maximum size for merging.
- setPadding(double) - Method in class TextStyle
-
Padding added around the text in both dimensions if a default size is inferred (ignored if an
explicit size is specified )
- setPadding(Padding) - Method in class DrawCroppedObjectsGenerator
-
- setPadding(Padding) - Method in class ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- setPaddingXY(int) - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY
directions
- setPaddingZ(int) - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- setPairAddCriteria(AddCriteriaPair) - Method in class EnergySchemeCreatorByElement
-
- setPairCollection(RandomCollection<IdentifiablePair<Mark>>) - Method in class KernelMerge
-
- setPairTypeClass(Class<?>) - Method in class RandomCollectionWithAddCriteria
-
- setParam(P) - Method in class PropertyInitializer
-
Sets the current parameters used for propagation
- setParamPrefix(String) - Method in class PermuteFeatureSequenceInteger
-
- setParamPrefixAppendNumber(boolean) - Method in class PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- setParams(HOGParameters) - Method in class HOGDescriptor
-
Parameters used for calculating HOG
- setParams(HOGParameters) - Method in class HOGFeature
-
Parameters used for calculating HOG
- setPath(String) - Method in class RootPath
-
A path on a filesystem to the directory, that defines the root
- setPath(String) - Method in class SingleFile
-
- setPath(String) - Method in class RootedFilePath
-
- setPath(String) - Method in class StaticFilePath
-
- setPathAnnotation(DerivePath) - Method in class SinglePathStrategy
-
- setPathDefaultMarks(DerivePath) - Method in class MarkProposerStrategy
-
- setPathLabel(DerivePath) - Method in class ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- setPathParams(DerivePath) - Method in class MarkProposerStrategy
-
- setPathParser(FilePathParser) - Method in class GroupFiles
-
- setPaths(StringSet) - Method in class FileSetFromStringSet
-
- setPaths(List<DerivePath>) - Method in class FilterForExistingFiles
-
All files need to be present
- setPenaltyValue(double) - Method in class MaxOverlapRatio
-
- setPeriodTriggerBank(PeriodTriggerBank<T>) - Method in class FeedbackBeginParameters
-
- setPermutation(AnchorBean<?>, Object) - Method in interface PermutationSetter
-
- setPermutation(AnchorBean<?>, Object) - Method in class PermutationSetterList
-
- setPermutation(AnchorBean<?>, Object) - Method in class PermutationSetterSingle
-
- setPermutation(PermuteProperty<S>) - Method in class PermuteFeature
-
A permutation to apply.
- setPermutations(List<PermuteProperty<S>>) - Method in class PermuteFeature
-
A list of permutations to apply.
- setPermuteProperty(PermuteProperty<?>) - Method in class Permute
-
- setPermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger
-
- setPhysical(boolean) - Method in class UnitConverter
-
- setPlotBackgroundColor(RGBColorBean) - Method in class PlotColorScheme
-
- setPlotGridlineColor(RGBColorBean) - Method in class PlotColorScheme
-
- setPoint(Point3i, int) - Method in class EncodedVoxels
-
- setPointConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
-
- setPointDirection(Point3i, int, int, int) - Method in class EncodedVoxels
-
- setPoints(Point3i, Point3i) - Method in class LineSegment
-
- setPoints(Point3d, Point3d) - Method in class LineSegment
-
- setPointsFitter(PointsFitter) - Method in class CreateMarkFromPoints
-
- setPointsFitter(String) - Method in class MarkProposerStrategy
-
- setPointsFitter(PointsFitter) - Method in class FitPoints
-
- setPointsFitter(PointsFitterToMark) - Method in class FitPointsFromObjects
-
- setPointsFitter(PointsFitter) - Method in class PointsFitterToMark
-
- setPointsFitter(PointsFitter) - Method in class ReflectInAxesWithinDistance
-
- setPointsFromOrientationProposer(PointsFromOrientationProposer) - Method in class MergeLists
-
- setPointsFromOrientationXYProposer(PointsFromOrientationProposer) - Method in class XYOrientationExtendToZ
-
- setPointsProposer(PointsProposer) - Method in class FitPoints
-
- setPosition(Point3d) - Method in class MarkWithPosition
-
- setPositionProposer(PositionProposer) - Method in class Position
-
- setPositionProposer(PositionProposer) - Method in class Repeat
-
- setPower(double) - Method in class MeanRaisedToPower
-
- setPrefix(String) - Method in class DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created
- setPrefix(boolean) - Method in class FromXmlList
-
If true, a prefix is prepended to the name of each added bean.
- setPrefix(String) - Method in class PermutePropertySequenceIntegerWithinString
-
- setPrefix(String) - Method in class PathPrefixerAvoidResolve
-
A string prefixed to each output-path.
- setPrefix(String) - Method in class DirectoryWithPrefix
-
Always prepended to outputted filenames.
- setPrefix(String) - Method in class ExperimentStructure
-
- setPrefixer(PathPrefixer) - Method in class OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- setPrefixer(PathPrefixerAvoidResolve) - Method in class LastDirectoryAsPrefix
-
- setPrefixer(PathPrefixerAvoidResolve) - Method in class Rooted
-
- setPrefixerElse(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is not true.
- setPrefixerIf(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is true.
- setPrefixToRemove(String) - Method in class DirectoryStructure
-
- setPrependColor(RGBColorBean) - Method in class Prepend
-
- setPrependString(String) - Method in class ListSequence
-
- setPrependString(String) - Method in class PrependName
-
- setPrependString(String) - Method in class DeriveFromPair
-
- setPrependString(String) - Method in class FeatureListProviderAggregatePair
-
- setPreserveAspectRatio(boolean) - Method in class ToDimensions
-
If true, the ratio between x and y is kept constant when scaling.
- setPreserveExtensionIfDuplicate(boolean) - Method in class RemoveExtension
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another
- setProbNeg(double) - Method in class KernelPosNeg
-
- setProbPos(double) - Method in class KernelPosNeg
-
- setProperty(String, Object) - Method in class ObjectWithProperties
-
- setPropertyPath(String) - Method in class PermutePropertyWithPath
-
Either a direct property of a bean e.g.
- setProposal(boolean) - Method in class VoxelizedMarksPeriodicReporter
-
- setProposer(MarkFromCollectionProposer) - Method in class MarkFromCollectionProposerUnary
-
- setProposer(MarkProposer) - Method in class MarkProposerUnary
-
- setProvider(MarkCollectionProvider) - Method in class FromProvider
-
- setPxlPartMemo(EnergyMemoList) - Method in class FeatureInputAllMemo
-
- setPxlPartMemo(VoxelizedMarkMemo) - Method in class FeatureInputSingleMemo
-
- setQuantile(double) - Method in class Quantile
-
The quantile.
- setQuantile(double) - Method in class QuantileStretch
-
- setQuantile(double) - Method in class Quantile
-
- setQuantile(double) - Method in class DiscardOutliers
-
- setQuantile(double) - Method in class Quantile
-
- setQuantile(double) - Method in class QuantileAcrossObjects
-
- setQuantile(double) - Method in class QuantileAcrossConnectedComponents
-
- setQuantileHigh(double) - Method in class Range
-
- setQuantileLow(double) - Method in class Range
-
- setQuantileLower(double) - Method in class ToByteUpperLowerQuantileIntensity
-
- setQuantileUpper(double) - Method in class ToByteUpperLowerQuantileIntensity
-
- setRadiiProposer(RadiiProposer) - Method in class OrientationAndRadiiProposer
-
- setRadiiProposer(RadiiProposer) - Method in class RadiiProposerRepeat
-
- setRadius(double) - Method in class MarkWithPositionAndSingleRadius
-
- setRadius(int) - Method in class AutoLocalThreshold
-
- setRadius(double) - Method in class WithRadiusBase
-
- setRadiusBound(Bound) - Method in class UniformRandomRadiiProposer
-
- setRadiusInMeters(boolean) - Method in class WithRadiusBase
-
- setRadiusX(double) - Method in class FitResult
-
- setRadiusY(double) - Method in class FitResult
-
- setRadiusZ(double) - Method in class FitResult
-
- setRate(double) - Method in class Geometry
-
- setReaderMatching(StackReader) - Method in class BranchExtension
-
The reader to use if the extension matches.
- setReaderNotMatching(StackReader) - Method in class BranchExtension
-
The reader to use if the extension does not match.
- setReceive(MaskProvider) - Method in class CombineBase
-
- setRecurseSubfolders(boolean) - Method in class MultiFileReader
-
- setRecursive(boolean) - Method in class SearchDirectory
-
If true the search is applied recursively over sub-directories.
- setRecursive(boolean) - Method in class ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- setRed(int) - Method in class RGBColorBean
-
- setRed(int) - Method in class RGBColor
-
- setRed(ChannelProvider) - Method in class ThreeChannels
-
- setReduce(FeatureListElem<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- setReduce(ReduceElements<ObjectMask>) - Method in class SuppressNonMaxima
-
The algorithm for reducing the number of object-masks.
- setReferencePoissonIntensity(double) - Method in class MarkWithIdentifierFactory
-
- setReferencesFeatureListCreator(StringSet) - Method in class ReferencedFeatures
-
Ensures any feature-lists mentioned here are evaluated, before this list is created.
- setReferencesFeatureListCreator(StringSet) - Method in class PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- setRegex(String) - Method in class RegularExpressionBase
-
- setRegEx(RegEx) - Method in class RegExMatcher
-
- setRegEx(RegEx) - Method in class PathRegEx
-
Regular expression to use to match path with at least one group in it.
- setRegEx(RegEx) - Method in class RemoveMatching
-
If a path matches a regular expression it is removed.
- setRegEx(RegEx) - Method in class Exclude
-
- setRegEx(RegEx) - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups.
- setRegEx(RegEx) - Method in class JoinRegExGroups
-
- setRegex(String) - Method in class Replace
-
Regular expression to match against string
- setRegex(String) - Method in class QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- setRegEx(RegEx) - Method in class ExperimentStructure
-
- setRegexAdjacent(String) - Method in class NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- setRegExDir(String) - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to directories
- setRegExFile(String) - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to files
- setRegExString(String) - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups, overloaded to handle legacy situations
where a string is supplied.
- setRegion(MarkRegion) - Method in class Thresholded
-
- setRegion(MarkRegion) - Method in class Intensity
-
- setRegionID(int) - Method in class VolumeMin
-
- setRegionID(int) - Method in class FromMarks
-
- setRegionID(int) - Method in class IndexedRegionBase
-
- setRegionID(int) - Method in class ColoredMarks
-
- setRegionID(int) - Method in class FeatureMarkRegion
-
- setRegionID(int) - Method in class FeatureSingleMemoRegion
-
- setRegionID(int) - Method in class FeaturePairMemoSingleRegion
-
- setRegionID(int) - Method in class KernelBirthAndKill
-
- setRegionMap(RegionMap) - Method in class EnergySchemeCreatorByElement
-
- setRegionMap(RegionMap) - Method in class FromMarks
-
- setRegionMap(RegionMap) - Method in class AsObject
-
- setRegionMap(RegionMap) - Method in class SurfaceSizeMaskNonZero
-
- setRejectIterationIfAllLow(boolean) - Method in class Erode
-
- setRejectIterationIfDisconnected(boolean) - Method in class Erode
-
- setRelation(RelationBean) - Method in class RelationToConstant
-
- setRelation(RelationBean) - Method in class ObjectFilterRelation
-
- setRelation(RelationBean) - Method in class MergePairs
-
Relation to threshold
- setRelation(RelationBean) - Method in class IdentityImposeValueRelationToHistogram
-
- setRelation(RelationToThreshold) - Method in class RejectIfConditionXYResolution
-
A predicate defined by the relationship of the XY-resolution to a constant threshold.
- setRelation(RelationBean) - Method in class AddCriteriaFeatureRelationThreshold
-
- setRelation(RelationBean) - Method in class RequireFeatureRelationThreshold
-
- setRelativeForIdentifier(boolean) - Method in class InputContextParams
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- setRemoveExtension(boolean) - Method in class FilePathPattern
-
if true, the extension is removed from paths before finding the pattern.
- setRemoveExtensionInDescription(boolean) - Method in class LastDirectories
-
Whether to remove the file-extension from the filename.
- setRemoveTouchingBorderXY(boolean) - Method in class FeatureCostAssigner
-
- setRepeat(int) - Method in class MovieFromSlices
-
- setRepeats(int) - Method in class KernelBirth
-
Total number of births
- setRepeatZProvider(Provider<Stack>) - Method in class GenerateString
-
Repeats the generated (2D) string in z, so it's the same z-extent as repeatZProvider
- setReplaceMatchesWithSolids(boolean) - Method in class CompareAnnotations
-
- setReplacement(String) - Method in class SubstituteRegularExpression
-
- setReplacement(String) - Method in class Replace
-
What to replace in the path
- setReplacement(String) - Method in class AdjacentFile
-
The replacement string used to determine the file
- setReplaceWithMidpoint(boolean) - Method in class MergeGreedyToIncreaseObjectFeature
-
- setReportFitterErrors(boolean) - Method in class FitPoints
-
- setRequireAllFilesMatch(boolean) - Method in class GroupFiles
-
- setRequireArguments(RequireArguments) - Method in class OnlyIf
-
The conditions that must be fulfilled
- setRequireArguments(RequireArguments) - Method in class FeedbackReceiverRequireArguments
-
- setRequireBBoxNeighbors(boolean) - Method in class MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or
touch
- setRequireTouching(boolean) - Method in class MergeWithFeature
-
Requires the object-masks to touch.
- setResizeTo(SizeXY) - Method in class GroupedMeanChannelTask
-
If set, each channel is scaled to a specific size before the mean is calculated (useful for
combining different sized images)
- setResizeTo(SizeXY) - Method in class HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- setResizeTo(SizeXY) - Method in class HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors
- setRestrictTo(MaskProvider) - Method in class Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this
mask
- setRewardHigherSide(boolean) - Method in class GaussianCumulative
-
Treat the higher side as if it's the the fill cdf
- setRewardLowerSide(boolean) - Method in class GaussianCumulative
-
- setRgb(boolean) - Method in class FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- setRoot1(double) - Method in class QuadraticEquationSolver.QuadraticRoots
-
- setRoot2(double) - Method in class QuadraticEquationSolver.QuadraticRoots
-
- setRootInStructure(boolean) - Method in class ExperimentResultsExperimentStructure
-
If true the directory structure is
ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory
structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- setRootName(String) - Method in class Rooted
-
The name of the root-path to associate with this fileset.
- setRootName(String) - Method in class RootedFilePath
-
- setRootName(String) - Method in class Rooted
-
- setRootName(String) - Method in class Rooted
-
- setRootName(String) - Method in class QuickBase
-
If non-empty then a rooted filesystem is used with this root
- setRootName(String) - Method in class RootedExperiment
-
Root-name assuming multi-rooted structure.
- setRootNameForStructure(String) - Method in class ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- setRootPath(Path) - Method in class RootDirectory
-
- setRotationAngle(Bound) - Method in class BoundRotation2D
-
- setRotationX(Bound) - Method in class BoundRotation3D
-
- setRotationY(Bound) - Method in class BoundRotation3D
-
- setRotationZ(Bound) - Method in class BoundRotation3D
-
- setRotMatrix(DoubleMatrix2D) - Method in class FitResult
-
- setRow(int) - Method in class Cell
-
- setSampleEvery(int) - Method in class SampleWithDirectory
-
- setScalarProposer(ScalarProposer) - Method in class MaxWithConstant
-
- setScalarProposer(ScalarProposer) - Method in class Scale
-
- setScale(double) - Method in class FirstSecondOrderStatistic
-
Standard-Deviation
- setScale(double) - Method in class MontageSlices
-
Whether to increase or reduce the size of the images
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
Determines how much to scale by
- setScaleCalculator(ScaleCalculator) - Method in class Scale
-
- setScaleCalculator(ScaleCalculator) - Method in class AtScale
-
- setScaleCalculator(ScaleCalculator) - Method in class Invert
-
- setScaleCalculator(ScaleCalculator) - Method in class ScaleImage
-
Calculates what scale-factor to apply on the image.
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
- setScaleFactor(double) - Method in class GradientBase
-
- setScaleInput(ScaleCalculator) - Method in class SegmentObjectsFromTensorFlowModel
-
Any scaling to be applied to the input-image before being input to the model for inference.
- setScaleLabel(boolean) - Method in class TileWithLabels
-
- setScaleLower(double) - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- setScaleLower(double) - Method in class ScaleByParams
-
- setScaleRadii(double) - Method in class ConicFitterBase
-
- setScaleUpper(double) - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- setScaleUpper(double) - Method in class ScaleByParams
-
- setScore(VoxelScore) - Method in class ScoreVoxels
-
- setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class ExtractSlice
-
- setScoreThreshold(double) - Method in class RemoveOverlappingObjects
-
Bounding boxes with scores above this threshold are removed
- setSecond(boolean) - Method in class ExperimentIdentifierAuto
-
Only relevant if time==true.
- setSecond(List<NamedBean<StringSet>>) - Method in class OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names)
- setSecond(StateTransformerBean<U, T>) - Method in class Compose
-
Second transformation from U to T
- setSecondary(boolean) - Method in class VoxelizedMarksPeriodicReporter
-
If proposal is true, this toggles between the primary and secondary proposal
- setSecondary(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class StateReporterToPixelized
-
- setSegment(BinarySegmentation) - Method in class BinarySegmentationOne
-
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary
-
- setSegment(BinarySegmentation) - Method in class SegmentChannel
-
Segmentation algorithm
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannel
-
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelByObject
-
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentStack
-
The segmentation procedure.
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentWithSeeds
-
- setSegment(BinarySegmentation) - Method in class ConnectedComponentsFromBinarySegmentation
-
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentInstanceWithModel
-
The segmentation algorithm
- setSegment(SegmentIntoMarks) - Method in class SegmentMarksFromImage
-
How to perform the segmentation.
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SuppressNonMaxima
-
The segmentation algorithm that is applied as an input to non-maxima suppression.
- setSegmentStack(BinarySegmentation) - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- setSelect(String) - Method in class DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- setSelectChannels(FromStacks) - Method in class GroupedStackBase
-
Selects which channels are included, optionally renaming.
- setSeparateEachLabel(boolean) - Method in class SuppressNonMaxima
-
If true, each label is reduced separately.
- setSeperator(String) - Method in class ListSequence
-
- setSeperator(String) - Method in class CombineCSV
-
- setSequence(SequenceInteger) - Method in class PermutePropertySequence
-
Where the sequence starts
- setSequence(SequenceInteger) - Method in class ListSequence
-
First number range that is appended
- setSequence(OutputSequenceIndexed<T, S>) - Method in class ChangeableOutputSequence
-
- setSequenceAdditional(SequenceInteger) - Method in class ListSequence
-
Another number range that is appended
- setSharedState(S) - Method in class SharedStateRememberConverted
-
The shared state.
- setShellRad(double) - Method in class MarkEllipseFactory
-
- setShellRad(double) - Method in class MarkEllipsoidFactory
-
- setShellRad(double) - Method in class Ellipse
-
- setShellRad(double) - Method in class Ellipsoid
-
- setShellRad(double) - Method in class FromObjects
-
- setShellRad(double) - Method in class CreateEllipse
-
- setShellRad(double) - Method in class ConicFitterBase
-
- setShowAgg(boolean) - Method in class MemoryUsageReporter
-
- setShowBest(boolean) - Method in class MemoryUsageReporter
-
- setShowDomainAxis(boolean) - Method in class BarPlot
-
- setShowOngoingJobsLessThan(int) - Method in class ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- setShowVerticalAxisLines(boolean) - Method in class PlotInstance
-
- setShuffle(boolean) - Method in class InputContextParams
-
If true, the order of the inputs are shuffled (randomized).
- setSigma(double) - Method in class BlurStrategy
-
- setSigma(double) - Method in class GaussianBlur2D
-
- setSigmaInMeters(boolean) - Method in class BlurStrategy
-
- setSilentlyDeleteExisting(boolean) - Method in class OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an
error.
- setSimplePairCollectionID(String) - Method in class KernelMerge
-
- setSize(SizeXY) - Method in class TextStyle
-
Explicit size of the image the string is draw on
- setSize(int) - Method in class Kernel
-
- setSize(double) - Method in class Aggregator
-
- setSize(SizeXY) - Method in class PlotHistogram
-
Size of the image produced showing a plot of the histogram
- setSize(SizeXY) - Method in class OutlinePreserveRelativeSize
-
Size of all created thumbnails
- setSize(SizeXY) - Method in class ScaleToSize
-
- setSize(SizeXY) - Method in class MovieFromSlices
-
- setSizeXY(SizeXY) - Method in class SpecifyDimensions
-
Length of X and Y dimensions.
- setSizeZ(int) - Method in class SpecifyDimensions
-
Length of Z dimension.
- setSkipAtBorder(boolean) - Method in class FillHoles
-
If true we do not fill any objects that touch the border
- setSkipFileName(boolean) - Method in class LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- setSkipFileName(boolean) - Method in class FilePathAppendBase
-
- setSkipFirstTrim(int) - Method in class RemoveTrailingDirectory
-
- setSkipFirstTrim(int) - Method in class FilePathAppendBase
-
- setSkipMissingChannels(boolean) - Method in class NamedChannelsAppend
-
- setSkipNumberSubdirectories(int) - Method in class LastDirectories
-
Initially skip this number of directories before including them in the description.
- setSlice(ChannelProvider) - Method in class RepeatSlice
-
- setSliceFirst(int) - Method in class MontageSlices
-
First slice.
- setSliceID(int) - Method in class SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- setSliceIndex(int) - Method in class RepeatSlice
-
Which slice to use from mask
- setSliceLast(int) - Method in class MontageSlices
-
Last slice.
- setSlicesSeparately(boolean) - Method in class FitBoxToOnVoxels
-
- setSmoothingFactor(double) - Method in class SplitContourAtSaddlePoints
-
- setSource(String) - Method in class StringMapItem
-
- setSource(FeatureSource<T, S, U>) - Method in class ExportFeatures
-
Source of feature-values to be exported
- setSplitDescriptiveNameRegex(String) - Method in class CompareAnnotations
-
- setSplitProposer(MarkSplitProposer) - Method in class KernelSplit
-
- setSquareSize(int) - Method in class SplitIntoSquares
-
- setStack(Provider<Stack>) - Method in class StackProviderUnary
-
- setStack(Provider<Stack>) - Method in class StackProviderWithLabel
-
- setStack(DisplayStack) - Method in class ColoredMarksWithDisplayStack
-
- setStack(DisplayStack) - Method in class MarksWithDisplayStack
-
- setStack(ProviderAsStack) - Method in class FromStack
-
Provides a stack.
- setStack(ProviderAsStack) - Method in class SegmentStack
-
The stack to segment
- setStack(StackProvider) - Method in class ExportObjectsFromCSV
-
The stack that is the background for our objects
- setStackAsChannel(boolean) - Method in class MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no
additionalChannel is set)
- setStackBackground(boolean) - Method in class VisualizeOnBackground
-
- setStackEnergy(Provider<Stack>) - Method in class FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- setStackEnergy(StackProvider) - Method in class FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is
considered to be the input stacks)
- setStackEnergy(StackProvider) - Method in class BinaryClassifierImageLabeller
-
- setStackEnergy(StackProvider) - Method in class ExtractSlice
-
- setStackEnergy(StackProvider) - Method in class DefineOutputterWithEnergy
-
- setStackID(String) - Method in class IfStackExists
-
- setStackName(String) - Method in class One
-
If defined, processing only occurs the stack with this specific stack and index.
- setStackNameVisualOriginal(String) - Method in class AnnotationBackground
-
- setStackProviderID(String) - Method in class FromStack
-
Specifies the ID of an existing stack.
- setStackProviderID(String) - Method in class FromStackChannel
-
- setStackReader(StackReader) - Method in class AnnotatorStrategy
-
- setStackReader(StackReader) - Method in class InputManagerWithStackReader
-
- setStackReader(StackReader) - Method in class MaskComparer
-
- setStackReader(StackReader) - Method in class FlattenAsChannel
-
Reads the image that is subsequently flattened.
- setStackReader(StackReader) - Method in class ImposeResolution
-
Reads an image before a resolution is imposed.
- setStackReader(StackReader) - Method in class MultiFileReader
-
- setStackReader(StackReader) - Method in class ReadVoxelExtentXml
-
Reads an image before a resolution is imposed.
- setStackReader(StackReader) - Method in class RejectIfConditionXYResolution
-
Reads an image before a resolution is imposed.
- setStackReaderAdjacent(StackReader) - Method in class NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- setStackReaderAppend(StackReader) - Method in class QuickBase
-
The raster-reader for reading any appended files
- setStart(int) - Method in class SequenceInteger
-
The index to begin iteration from
- setStartIndex(int) - Method in class MovieFromSlices
-
- setStartingIntensity(int) - Method in class FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- setStateReporter(StateReporter<T, S>) - Method in class TransformationAssignMode
-
- setStrategy(BlurStrategy) - Method in class Blur
-
- setStringRasterGenerator(TextStyle) - Method in class GenerateString
-
- setStrongEdgeEnhancer(boolean) - Method in class AnisotropicDiffusion
-
Enables the StrongEdgeEnhancer diffusion function
- setSubdirectory(String) - Method in class AppendDictionary
-
- setSubdirectory(String) - Method in class ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix
${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- setSubtractConstant(int) - Method in class IntensityGradientBase
-
- setSubtractFromMaskOnly(boolean) - Method in class SubtractMean
-
- setSubtractRadii(double) - Method in class ConicFitterBase
-
- setSuffix(String) - Method in class PermutePropertySequenceIntegerWithinString
-
- setSummarizer(Summarizer<S>) - Method in class SummarizerInputFromManager
-
- setSummarizer(Summarizer<S>) - Method in class SummarizeBase
-
- setSummarizerElse(Summarizer<T>) - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) <= countThreshold
- setSummarizerGreaterThan(Summarizer<T>) - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) > countThreshold
- setSuppress3D(boolean) - Method in class MorphologicalOperatorBase
-
- setSuppress3D(boolean) - Method in class SurfaceNumberVoxelsBase
-
- setSuppress3D(boolean) - Method in class SegmentThresholdAboveMinBound
-
- setSuppressDirectories(boolean) - Method in class FromDescriptiveName
-
If true, any directory separators in the identifier in a descriptive-name are replaced by
underscores.
- setSuppressErrors(boolean) - Method in class FromObjects
-
- setSuppressExceptions(boolean) - Method in class JobProcessor
-
- setSuppressExceptions(boolean) - Method in class QuickMultiDatasetExperiment
-
- setSuppressExceptions(boolean) - Method in class QuickMultiDatasetStructuredExperiment
-
- setSuppressOutlineZ(boolean) - Method in class ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- setSuppressRes(boolean) - Method in class RadiiRatio
-
- setSuppressRootOut(boolean) - Method in class Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against
the location of the BeanXML.
- setSuppressSeries(boolean) - Method in class ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- setSuppressSubfolders(boolean) - Method in class DefineOutputter
-
- setSuppressZ(boolean) - Method in class BoundingBoxIntersection
-
- setSuppressZ(boolean) - Method in class DistanceTransform3D
-
- setSuppressZ(boolean) - Method in class DistanceTransformForEachObject3D
-
- setSuppressZ(boolean) - Method in class MergeWithOptionalDistanceConstraint
-
- setSuppressZ(boolean) - Method in class CostOverlapWithinMidpointDistance
-
- setSuppressZ(boolean) - Method in class ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- setSuppressZ(boolean) - Method in class CenterOnMask
-
- setSuppressZ(boolean) - Method in class UniformRandom
-
- setSuppressZ(boolean) - Method in class SurfaceSizeMaskNonZero
-
- setSuppressZ(boolean) - Method in class EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- setSuppressZCovariance(boolean) - Method in class FromObjects
-
- setSuppressZCovariance(boolean) - Method in class LinearLeastSquaresEllipsoidFitter
-
- setTarget(String) - Method in class StringMapItem
-
- setTask(Task<T, S>) - Method in class JobProcessor
-
- setTask(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setTask(Task<U, S>) - Method in class ConvertNamedChannels
-
The underlying task that will be called, perhaps with a different input-type.
- setTask(Task<MultiInput, S>) - Method in class QuickExperiment
-
- setTask(Task<T, S>) - Method in class QuickMultiDatasetExperiment
-
- setTask(Task<T, S>) - Method in class QuickMultiDatasetStructuredExperiment
-
- setTaskProcessor(JobProcessor<T, S>) - Method in class InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- setTemperature(double) - Method in class OptimizationStep
-
- setTemplateMark(MarkFactory) - Method in class MarkWithIdentifierFactory
-
- setTermination(TerminationCondition) - Method in class SimulatedAnnealing
-
- setText(String) - Method in class GenerateString
-
Text to draw on an image
- setThreshold(double) - Method in class RelationToConstant
-
- setThreshold(int) - Method in class CutBelowThreshold
-
- setThreshold(int) - Method in class CalculateLevelRelativeToThreshold
-
- setThreshold(UnitValueDistance) - Method in class IntensityGreaterEqualThan
-
- setThreshold(double) - Method in class ThresholdedFeature
-
- setThreshold(UnitValueVolume) - Method in class ThresholdedVolume
-
- setThreshold(RelationToThreshold) - Method in class Count
-
- setThreshold(RelationToThreshold) - Method in class RatioThreshold
-
- setThreshold(double) - Method in class FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- setThreshold(double) - Method in class AddCriteriaFeatureRelationThreshold
-
- setThreshold(double) - Method in class RequireFeatureRelationThreshold
-
- setThreshold(RelationToThreshold) - Method in class GreatestAreaSlice
-
- setThreshold(RelationToThreshold) - Method in class Thresholded
-
- setThreshold(RelationToThreshold) - Method in class IfCondition
-
- setThresholder(Thresholder) - Method in class BinarySegmentationThreshold
-
- setThresholder(Thresholder) - Method in class Threshold
-
The thresholder that will convert a channel into a binary-channel
- setThrowExceptionForInsufficientPoints(boolean) - Method in class CreateMarkFromPoints
-
- setThumbnail(ThumbnailFromObjects) - Method in class CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more objects combine, as form a single input
- setThumbnail(ThumbnailFromStack) - Method in class FromImage
-
Method to generate a thumbnail for images
- setTime(boolean) - Method in class ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output
- setTimeIndex(int) - Method in class ConvertNamedChannelsToStack
-
- setTimeIndexGroupID(int) - Method in class RegularExpression
-
- setTimes(int) - Method in class Repeat
-
- setTitle(String) - Method in class ReportFeatureEvaluator
-
- setTitle(String) - Method in class ReportFeatureForManifestFileBase
-
- setTolerance(int) - Method in class UnchangedScore
-
An exponent of 10 which determines a tolerance, less than which a score will be deemed
unchanged compared to another.
- setTransformer(StateTransformerBean<MarkCollection, T>) - Method in class RemovePartitionAndThen
-
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class VoxelizeWithTransform
-
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class KernelStateBridgePixelize
-
- setTransformerKernelToState(StateTransformerBean<U, T>) - Method in class KernelStateBridgeTransformer
-
- setTransformerMarks(StateTransformerBean<MarkCollection, VoxelizedMarksWithEnergy>) - Method in class AddDualTransformer
-
- setTransformerPrimary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer
-
- setTransformerSecondary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer
-
- setTransformerStateToKernel(StateTransformerBean<T, U>) - Method in class KernelStateBridgeTransformer
-
- setTransposed(boolean) - Method in class CombineCSV
-
- setTrimTrailingDirectory(int) - Method in class RemoveTrailingDirectory
-
- setTrimTrailingDirectory(int) - Method in class FilePathAppendBase
-
- setUniqueLabel(String) - Method in class AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- setUnit(UnitConverter) - Method in class BoundingBoxExtent
-
- setUnit(UnitConverter) - Method in class FeatureSingleMemoRegion
-
- setUnitType(String) - Method in class DistancePhysical
-
- setUnitType(String) - Method in class AreaPhysical
-
- setUnitType(String) - Method in class VolumePhysical
-
- setUnitType(String) - Method in class FeatureConvertUnits
-
- setUnitType(String) - Method in class UnitConverter
-
- setUnitTypeFrom(String) - Method in class ConvertUnits
-
- setUnitTypeTo(String) - Method in class ConvertUnits
-
- setUnitValueDistance(UnitValueDistance) - Method in class FromUnitValueDistance
-
- setupBefore(Dimensions, int) - Method in class ConvertTo
-
- setupBefore(Dimensions, int) - Method in class ToUnsignedByte
-
- setupBefore(Dimensions, int) - Method in class UnsignedByteFromUnsignedByteInterleaving
-
- setupBefore(Dimensions, int) - Method in class UnsignedByteFromUnsignedInt
-
- setupBefore(Dimensions, int) - Method in class UnsignedByteFromUnsignedShort
-
- setupBefore(Dimensions, int) - Method in class ToFloat
-
- setupBefore(Dimensions, int) - Method in class UnsignedIntFromUnsignedInt
-
- setupBefore(Dimensions, int) - Method in class ToUnsignedShort
-
- setupParams(Dictionary) - Method in class FromDictionaryBase
-
- setUseLastSeriesIndexOnly(boolean) - Method in class NamedChannels
-
- setUseLastSeriesIndexOnly(boolean) - Method in class Stacks
-
- setUseMax(boolean) - Method in class OverlapRatio
-
- setUseMax(boolean) - Method in class OverlapRatioMask
-
- setUseMIP(boolean) - Method in class MultipleComparer
-
- setUseMIP(boolean) - Method in class CompareAnnotations
-
- setUserFriendlyLabel(String) - Method in class AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- setUseZ(boolean) - Method in class RemoveTouchingBorder
-
- setUseZ(boolean) - Method in class TraverseOutlineOnImage
-
- setValue(T) - Method in class NamedBean
-
- setValue(T) - Method in interface NameValue
-
Sets the associated value
- setValue(V) - Method in class SimpleNameValue
-
- setValue(double) - Method in class Constant
-
- setValue(double) - Method in class DistancePhysical
-
- setValue(double) - Method in class DistanceVoxels
-
- setValue(double) - Method in class UnitValueArea
-
- setValue(double) - Method in class VolumePhysical
-
- setValue(double) - Method in class VolumeVoxels
-
- setValue(double) - Method in class AssignValue
-
- setValue(int) - Method in class CreateNew
-
- setValue(double) - Method in class UnaryWithValueBase
-
- setValue(int) - Method in class EmptyHistogramConstant
-
- setValue(String) - Method in class IfParamEqual
-
- setValue(String) - Method in class DictionaryCondition
-
The value the key should have in the dictionary, in order for the condition to be fulfilled.
- setValue(double) - Method in class ConstantScaleFactor
-
- setValue(int) - Method in class CountEqual
-
- setValue(double) - Method in class IdentityImposeValueRelationToHistogram
-
- setValue(double) - Method in class NormalizeByConstant
-
- setValue(String) - Method in class Constant
-
- setValue(double) - Method in class Constant
-
- setValue(double) - Method in class WithValueBase
-
- setValueByDimension(int, double) - Method in class Tuple3d
-
- setValueByDimension(int, float) - Method in class Tuple3f
-
- setValueIfEmpty(double) - Method in class FeatureHistogramStatistic
-
The value to return iff exceptionifEmpty is false
- setValueIfTooFewVoxels(double) - Method in class ImageMomentsBase
-
A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate
moments
- setValueNoObject(int) - Method in class ScoreObjects
-
- setValueNoObjects(double) - Method in class FeatureIntersectingObjects
-
- setValues(StringSet) - Method in class PermutePropertyDoubleSet
-
- setValues(StringSet) - Method in class PermutePropertyStringSet
-
The values of the string-set
- setVaryColors(boolean) - Method in class SegmentInstanceWithModel
-
If true the colors change for different objects in the image (using a default color set).
- setVersion(String) - Method in class ExperimentIdentifierConstant
-
- setVerticalAlign(String) - Method in class Overlay
-
- setVisitScheduler(VisitScheduler) - Method in class TraverseOutlineOnImage
-
- setWeight(double) - Method in class KernelProposerOptionSingle
-
- setWeightBackground(double) - Method in class OtsuWeighted
-
- setWeightForeground(double) - Method in class OtsuWeighted
-
- setWeightItem1Greater(double) - Method in class Range
-
- setWeightItem2Greater(double) - Method in class Range
-
- setWeightNegative(double) - Method in class KernelProposerOptionDual
-
- setWeightPositive(double) - Method in class KernelProposerOptionDual
-
- setWeightWidthDescription(int) - Method in class WholeImageLabelStrategy
-
- setWhenBinaryChannel(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled binary image.
- setWhenDetailed(LoggingDestination) - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- setWhenEqual(ObjectCollectionProvider) - Method in class IfParamEqual
-
- setWhenFalse(DrawObject) - Method in class IfElse
-
- setWhenNot(LoggingDestination) - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- setWhenNotEqual(ObjectCollectionProvider) - Method in class IfParamEqual
-
- setWhenRelative(FileNamer) - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is selected.
- setWhenRGB(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled RGB image.
- setWhenSingleChannel(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
- setWhenThreeChannels(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled non-RGB image.
- setWhenTrue(DrawObject) - Method in class IfElse
-
- setWidth(int) - Method in class SizeXY
-
Size in X dimension.
- setWidth(double) - Method in class Difference
-
Width (what the difference is divided by)
- setWidth(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in x-dimension.
- setWidthFactor(double) - Method in class DifferenceCalculateLevelStandardDeviation
-
- setWindowSize(int) - Method in class CenterSliceWindow
-
- setWindowSize(SizeXY) - Method in class HOGParameters
-
The window-size as per OpenCV implementation.
- setWithin(double) - Method in class UnitsWithinRange
-
Returned as a constant if a value lies within the range
- setWithinValue(double) - Method in class CompareWithRange
-
Constant to return if value lies within the range
- setWithinValue(double) - Method in class CompareWithRangeFeature
-
Constant to return if value lies within the range
- setWriter(DrawObject) - Method in class Flatten
-
- setWriter(StackWriter) - Method in class BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- setWriter(StackWriter) - Method in class WriteResolutionXml
-
- setWriterAlways2D(StackWriter) - Method in class BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- setWriterElse(StackWriter) - Method in class BranchStack
-
Otherwise the writer to use.
- setWriterIfNoSuggestion(StackWriter) - Method in class BranchSuggestedFormat
-
The writer to use if there is no suggested file-format.
- setWriters(List<NamedBean<?>>) - Method in class OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
- setWritersIfSuggested(List<StackWriter>) - Method in class BranchSuggestedFormat
-
A list of writers to select if a given format is used
- setX(double) - Method in class VectorInDirection
-
- setX(String) - Method in class PlotAxisLabels
-
- setX(int) - Method in class Point2i
-
- setX(int) - Method in class Tuple3d
-
- setX(double) - Method in class Tuple3d
-
- setX(int) - Method in class Tuple3i
-
- setXDiv(double) - Method in class Orientation
-
- setXY(String, String) - Method in class PlotAxisLabels
-
- setY(double) - Method in class VectorInDirection
-
- setY(String) - Method in class PlotAxisLabels
-
- setY(int) - Method in class Point2i
-
- setY(int) - Method in class Tuple3d
-
- setY(double) - Method in class Tuple3d
-
- setY(int) - Method in class Tuple3i
-
- setYAxisLowerMargin(double) - Method in class LinePlot
-
- setYAxisMargins(double) - Method in class LinePlot
-
- setYAxisUpperMargin(double) - Method in class LinePlot
-
- setYValGetter(LinePlot.YValGetter<T>) - Method in class LinePlot
-
- setZ(double) - Method in class VectorInDirection
-
- setZ(int) - Method in class Tuple3d
-
- setZ(double) - Method in class Tuple3d
-
- setZ(int) - Method in class Tuple3i
-
- setZAlign(String) - Method in class Overlay
-
- setZSliceGroupID(int) - Method in class RegularExpression
-
- setZSliceNum(int) - Method in class SortedSetSlice
-
- shallowCopy() - Method in class ColorList
-
- shallowCopy() - Method in class GraphWithPayload
-
Creates a new graph with identical elements and structure, reusing the existing vertice and
edge data objects.
- shallowCopy() - Method in class FeatureNameList
-
- shallowCopy() - Method in class RandomCollectionWithAddCriteria
-
- shallowCopy() - Method in class MarksWithEnergyBreakdown
-
- shallowCopy() - Method in class MarksWithTotalEnergy
-
Make a shallow copy
- shallowCopy() - Method in class VoxelizedMarksWithEnergy
-
Creates a shallow-copy of the marks
- shallowCopy() - Method in class EnergySavedAll
-
- shallowCopy() - Method in class EnergySavedInd
-
- shallowCopy() - Method in class EnergySavedPairs
-
- shallowCopy() - Method in class ColoredMarks
-
- shallowCopy() - Method in class MarkCollection
-
- shallowCopy() - Method in class OverlayCollection
-
- shallowDuplicate() - Method in class FeatureList
-
Creates a new feature-list which contains identical elements
- ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ShapeRegularityCenterSlice() - Constructor for class ShapeRegularityCenterSlice
-
- ShapeRegularityMIP - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ShapeRegularityMIP() - Constructor for class ShapeRegularityMIP
-
- SharedFeatureMulti - Class in org.anchoranalysis.feature.shared
-
A group of features (of possibly heterogeneous type) made available to other features to
reference
- SharedFeatureMulti() - Constructor for class SharedFeatureMulti
-
- SharedFeatureSet<T extends FeatureInput> - Class in org.anchoranalysis.feature.shared
-
- SharedFeatureSet(NameValueSet<Feature<T>>) - Constructor for class SharedFeatureSet
-
- SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store
-
Objects shared between different components.
- SharedObjects(CommonContext) - Constructor for class SharedObjects
-
- sharedObjectsRequired() - Method in class FeatureInitialization
-
- SharedStateExportFeatures<S> - Class in org.anchoranalysis.plugin.image.task.feature
-
Shared-state for an export-features class
- SharedStateExportFeatures(ResultsWriterMetadata, Supplier<S>, InputOutputContext) - Constructor for class SharedStateExportFeatures
-
Creates the shared state.
- SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller
-
- SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>, String, String) - Constructor for class SharedStateFilteredImageOutput
-
- SharedStateRememberConverted<U extends InputFromManager,S> - Class in org.anchoranalysis.plugin.mpp.experiment
-
Shared-state that remembers converted inputs for corresponding unconverted inputs.
- SharedStateRememberConverted() - Constructor for class SharedStateRememberConverted
-
- SharedStateSegmentInstance<T> - Class in org.anchoranalysis.plugin.image.task.segment
-
Shared-state for instance segmentation
- SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, InputOutputContext) - Constructor for class SharedStateSegmentInstance
-
- SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.stack
-
- SharedStateSelectedSlice(Outputter) - Constructor for class SharedStateSelectedSlice
-
- Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
- Shell() - Constructor for class Shell
-
- shift() - Method in class SlidingBuffer
-
Increments the slice number by one
- shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class VoxelsAssignerFactory
-
Shifts all coordinates BACKWARDS before passing to another
VoxelsAssigner.
- shiftBackBy(ReadableTuple3i) - Method in class ObjectMask
-
Shifts the object-mask by moving its bounding-box backwards (i.e.
- shiftBackBy(ReadableTuple3i) - Method in class BoundingBox
-
Shifts the bounding-box backwards.
- shiftBy(T, ReadableTuple3i) - Method in interface AccessObjectMask
-
Positionally-shifts an element by a given quantity in the positive direction.
- shiftBy(ReadableTuple3i) - Method in class ObjectCollection
-
Shifts the bounding-box of each object by adding to it i.e.
- shiftBy(ReadableTuple3i) - Method in class ObjectMask
-
Shifts the object-mask by moving its bounding-box forwards (i.e.
- shiftBy(ReadableTuple3i) - Method in class BoundingBox
-
Shifts the bounding-box forwards.
- shiftTo(Point3i) - Method in class BoundingBox
-
Assigns a new corner-location to the bounding-box.
- shiftToOrigin() - Method in class ObjectMask
-
Creates a new object-mask with identical voxels but with the bounding-box beginning at the
origin (0,0,0)
- shiftToOrigin() - Method in class BoundingBox
-
Moves the bounding-box to the origin (0,0,0) but preserves the extent
- shiftToZ(int) - Method in class BoundingBox
-
Assigns a new z-slice corner-location to the bounding-box
- SHORT_OPTION_DEBUG - Static variable in class CommandLineOptions
-
Enables debug-mode: runs only the first available input [whose name contains string].
- SHORT_OPTION_HELP - Static variable in class CommandLineOptions
-
Displays help message with all command-line options.
- SHORT_OPTION_INPUT - Static variable in class CommandLineOptions
-
Changes inputs.
- SHORT_OPTION_INPUT_COPY_NON_INPUTS - Static variable in class CommandLineOptions
-
Additionally copies any files in the input directory, unused as inputs.
- SHORT_OPTION_INPUT_RELATIVE - Static variable in class CommandLineOptions
-
Derives the unique identifier from the **entire relative filename or path** (excluding file
extension).
- SHORT_OPTION_INPUT_SHUFFLE - Static variable in class CommandLineOptions
-
Shuffles the order of the inputs.
- SHORT_OPTION_INPUT_SUBSET_IDENTIFIER - Static variable in class CommandLineOptions
-
Subsets the identifier.
- SHORT_OPTION_LOG_ERROR - Static variable in class CommandLineOptions
-
Logs initial BeanXML errors in greater detail to a file-path.
- SHORT_OPTION_OUTPUT - Static variable in class CommandLineOptions
-
Changes output manager.
- SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class CommandLineOptions
-
Disables specific output(s).
- SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class CommandLineOptions
-
Enables all outputs.
- SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class CommandLineOptions
-
Enables specific output(s).
- SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT - Static variable in class CommandLineOptions
-
Suggests an output image file format: e.g -of jpg or -of ome.xml.
- SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER - Static variable in class CommandLineOptions
-
Outputs with an incrementing number instead of the input identifier.
- SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER - Static variable in class CommandLineOptions
-
Ignores the experiment identifier, when forming an output-path.
- SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES - Static variable in class CommandLineOptions
-
Suppressed the subdirectory structure when outputting file identifiers.
- SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class CommandLineOptions
-
Shows additional argument information, otherwise executes as normal.
- SHORT_OPTION_SHOW_TASKS - Static variable in class CommandLineOptions
-
Prints the names of predefined tasks that can be easily used with -t.
- SHORT_OPTION_TASK - Static variable in class CommandLineOptions
-
Changes task.
- SHORT_OPTION_TASK_NUMBER_PROCESSORS - Static variable in class CommandLineOptions
-
Suggests a maximum number of processors to use for the task.
- SHORT_OPTION_TASK_SIZE - Static variable in class CommandLineOptions
-
Suggests dimensions or a scaling factor for certain tasks.
- SHORT_OPTION_VERSION - Static variable in class CommandLineOptions
-
Displays version and authorship information.
- shouldObjectsBeProcessed(ObjectMask, ObjectMask) - Method in class ConditionallyMergeOverlappingObjects
-
- shouldObjectsBeProcessed(ObjectMask, ObjectMask) - Method in class ReduceElementsGreedy
-
Whether to include another (possibly-overlapping with source) element in processing?
- shouldObjectsBeProcessed(ObjectMask, ObjectMask) - Method in class RemoveOverlappingObjects
-
- shouldOverwriteVoxelWithConstant(int, int) - Method in class ArithmeticWithConstantConditionallyWriteBase
-
Whether to overwrite the current voxel-value with the constant?
- shouldOverwriteVoxelWithConstant(int, int) - Method in class MaxWithConstant
-
- shouldOverwriteVoxelWithConstant(int, int) - Method in class MinWithConstant
-
- Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme
-
Randomizes the order of the colors from existing scheme.
- Shuffle(ColorScheme) - Constructor for class Shuffle
-
- Shuffle() - Constructor for class Shuffle
-
- shuffle() - Method in class ColorList
-
- Shuffle<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Randomly shuffles the order of an input-manager
- Shuffle() - Constructor for class Shuffle
-
- ShuffleIfRequested<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
- ShuffleIfRequested() - Constructor for class ShuffleIfRequested
-
- SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
-
- SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
-
- SignedVoxelType(int, String, long, long) - Constructor for class SignedVoxelType
-
- SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io
-
Deletes any annotation that is only the file represented at the path
- SimpleAnnotationDeleter() - Constructor for class SimpleAnnotationDeleter
-
- SimpleManifestDeserializer - Class in org.anchoranalysis.io.manifest.deserializer
-
- SimpleManifestDeserializer() - Constructor for class SimpleManifestDeserializer
-
- SimpleName - Class in org.anchoranalysis.feature.io.name
-
A name with only one part, and is always unique.
- SimpleName(String) - Constructor for class SimpleName
-
- SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name
-
A simple container expressing a name-value pair
- SimpleNameValue(String, V) - Constructor for class SimpleNameValue
-
- SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- SimpleOutputNameStyle(String) - Constructor for class SimpleOutputNameStyle
-
- SimpleOverlayWriter - Class in org.anchoranalysis.mpp.io.marks.generator
-
Converts a configuration to a set of object-masks, using a simple
DrawObject for all
objects.
- SimpleOverlayWriter(DrawObject) - Constructor for class SimpleOverlayWriter
-
- SimplePropertyDefiner<P> - Class in org.anchoranalysis.bean.initializable.property
-
- SimplePropertyDefiner(Class<?>) - Constructor for class SimplePropertyDefiner
-
- SimulatedAnnealing<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
Finds an optima using a simulated-annealing approach
- SimulatedAnnealing() - Constructor for class SimulatedAnnealing
-
- Single - Class in org.anchoranalysis.image.bean.spatial.arrange
-
- Single() - Constructor for class Single
-
- Single - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- Single() - Constructor for class Single
-
- SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
A score that is calculated on a single channel only
- SingleChannel() - Constructor for class SingleChannel
-
- SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
For an image with a single channel
- SingleChannel() - Constructor for class SingleChannel
-
- SingleChannel(String) - Constructor for class SingleChannel
-
- singleChannelMaybe3D(boolean) - Static method in class StackWriteAttributesFactory
-
- SingleColor - Class in org.anchoranalysis.core.color
-
An index that always uses the same single color
- SingleColor(Color) - Constructor for class SingleColor
-
- SingleColor(RGBColor) - Constructor for class SingleColor
-
- SingleContainer<T> - Class in org.anchoranalysis.core.index.bounded
-
- SingleContainer(boolean) - Constructor for class SingleContainer
-
- SingleContainer(T, int, boolean) - Constructor for class SingleContainer
-
- SingleFile - Class in org.anchoranalysis.io.input.bean.files
-
- SingleFile(String) - Constructor for class SingleFile
-
- SingleFile() - Constructor for class SingleFile
-
- SingleFileInputBase - Class in org.anchoranalysis.io.input.file
-
A base class for inputs that refer to a single file.
- SingleFileInputBase(NamedFile) - Constructor for class SingleFileInputBase
-
- SingleFileTypeGenerator<T,S> - Class in org.anchoranalysis.io.generator
-
A
Generator that eventually writes only a single file to the filesystem.
- SingleFileTypeGenerator() - Constructor for class SingleFileTypeGenerator
-
- SingleFileTypeGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator
-
Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
- SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class SingleFileTypeGeneratorBridge
-
- SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelAnd
-
- SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelBinary
-
- SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single
-
Outputs are enabled if they are contained in a set.
- SingleLevelInSet(Set<String>) - Constructor for class SingleLevelInSet
-
- SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class SingleLevelNot
-
- SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelOr
-
- SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single
-
- SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider
-
Provides (maybe) a single mark
- SingleMarkProvider() - Constructor for class SingleMarkProvider
-
- SingleObjectFromChannelFactory - Class in org.anchoranalysis.image.core.object.factory
-
- SingleObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object.factory
-
- SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
- SinglePathStrategy() - Constructor for class SinglePathStrategy
-
- singleProcessor() - Static method in class ConcurrencyPlan
-
Creates a plan for a single-CPU processor with the default number of GPUs.
- singleProcessor(int) - Static method in class ConcurrencyPlan
-
Creates a plan for a single-CPU processor - with a maximum number of GPUs.
- SingleRowPerInput<T extends InputFromManager,S extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
-
Base class for exporting features, where features are calculated per-image using a
NamedFeatureStore.
- SingleRowPerInput(String) - Constructor for class SingleRowPerInput
-
- SingleTableCalculator - Class in org.anchoranalysis.image.feature.calculator
-
- SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class SingleTableCalculator
-
- size() - Method in class ColorList
-
- size() - Method in class NameValueSet
-
- size() - Method in class FeatureList
-
- size() - Method in class FeatureNameList
-
- size() - Method in class ResultsVectorList
-
- size() - Method in class NamedFeatureStore
-
- size() - Method in class ObjectCollectionWithProperties
-
- size() - Method in class ScaledElements
-
Number of scaled-elements.
- size() - Method in class SeedCollection
-
- size() - Method in class ContiguousVoxelPath
-
- size() - Method in class LoopablePoints
-
- size() - Method in class NamedStacks
-
Number of stacks
- size() - Method in class TimeSequence
-
- size() - Method in class StackSeries
-
- size() - Method in class IntersectingObjects
-
Number of items in the r-tree.
- size() - Method in class ObjectCollection
-
- size() - Method in interface VoxelStatistics
-
- size() - Method in class VoxelStatisticsCombined
-
- size() - Method in class VoxelStatisticsFromHistogram
-
- size() - Method in class VoxelsWrapperList
-
- size() - Method in class Histogram
-
The number of items in the histogram (maxBin - minBin + 1)
- size() - Method in class BoundUnitless
-
- size() - Method in class MarksWithEnergyBreakdown
-
- size() - Method in class MarksWithTotalEnergy
-
- size() - Method in class VoxelizedMarksWithEnergy
-
- size() - Method in class EnergySavedInd
-
- size() - Method in class EnergyMemoList
-
- size() - Method in class MemoList
-
- size() - Method in class UpdatableMarksList
-
- size() - Method in class IndexByChannel
-
- size() - Method in class ColoredMarks
-
- size() - Method in class MarkCollection
-
- size() - Method in interface MemoForIndex
-
- size() - Method in class TerminationConditionListOr
-
- size() - Method in class WeightedKernelList
-
- size() - Method in class ColoredOverlayCollection
-
- size() - Method in class OverlayCollection
-
- size() - Method in class ListWithThumbnails
-
- size() - Method in class ParsedFilePathBag
-
- Size - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- Size() - Constructor for class Size
-
- size() - Method in class BoundedList
-
The number of elements
- size() - Method in class RTree
-
The total number of items stored in the tree.
- sizeBytes - Variable in class ToUnsignedByte
-
- sizeC(IFormatReader) - Method in class Default
-
- sizeC(IFormatReader) - Method in class ForceNumberChannels
-
- sizeC(IFormatReader) - Method in class ReadOptions
-
Number of channels.
- sizeC(IFormatReader) - Method in class ReadOptionsDelegate
-
- sizeCurrentLoad() - Method in class LRUCache
-
Number of items currently in the cache
- sizeCurrentLoad() - Method in class FeatureCalculatorCachedMulti
-
Number of items currently in the cache
- sizeDescriptor(Extent) - Method in class HOGParameters
-
Calculates the size of the descriptor will be for a given image, assuming the window is equal
to the image-size
- SizeExtents - Class in org.anchoranalysis.plugin.io.multifile
-
Remembers the different sizes among the files
- SizeExtents(ParsedFilePathBag) - Constructor for class SizeExtents
-
- sizeFeatures() - Method in class FeatureCalculatorCachedMulti
-
- sizeFeatures() - Method in interface FeatureCalculatorMulti
-
The number of features that is calculated on each call to calc(), and therefore the size of
the ResultsVector returned
- sizeFeatures() - Method in class FeatureCalculatorMultiChangeInput
-
- sizeFeatures() - Method in class SequentialSession
-
- sizeFeatures() - Method in class PairsTableCalculator
-
- sizeFeatures() - Method in class SingleTableCalculator
-
- sizeFirst() - Method in class CostMatrix
-
The number of elements in the first list.
- sizeSecond() - Method in class CostMatrix
-
The number of elements in the second list.
- sizeT(Progress) - Method in interface NamedChannelsForSeries
-
- sizeT(Progress) - Method in class NamedChannelsForSeriesConcatenate
-
- sizeT(Progress) - Method in class NamedChannelsForSeriesMap
-
- sizeT(IFormatReader) - Method in class Default
-
- sizeT(IFormatReader) - Method in class ForceNumberFrames
-
- sizeT(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- sizeT(IFormatReader) - Method in class ReadOptions
-
Number of time-points (frames in a time series).
- sizeT(IFormatReader) - Method in class ReadOptionsDelegate
-
- SizeXY - Class in org.anchoranalysis.image.bean.spatial
-
- SizeXY(Extent) - Constructor for class SizeXY
-
Constructor
- SizeXY() - Constructor for class SizeXY
-
- SizeXY(int, int) - Constructor for class SizeXY
-
- sizeXY - Variable in class ToUnsignedByte
-
- sizeZ(IFormatReader) - Method in class Default
-
- sizeZ(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- sizeZ(IFormatReader) - Method in class ReadOptions
-
Number of z-slices (slices in a 3D image).
- sizeZ(IFormatReader) - Method in class ReadOptionsDelegate
-
- skewness(Histogram) - Static method in class HistogramStatistics
-
- Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- Skewness() - Constructor for class Skewness
-
- SkipInit - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that this particular bean-field should be ignored during (recursive) initialisation
- slice(int) - Method in class BinaryVoxels
-
- slice(int) - Method in class FromByte
-
- slice(int) - Method in class FromFloat
-
- slice(int) - Method in class FromInt
-
- slice(int) - Method in class FromShort
-
- slice(int) - Method in interface SliceBufferIndex
-
- slice(int) - Method in class Base
-
- slice(int) - Method in interface VoxelsExtracter
-
Creates a new
Voxels with only particular slice
- slice(int) - Method in class Voxels
-
- slice(int) - Method in class VoxelsWrapper
-
- SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
-
- SliceAt() - Constructor for class SliceAt
-
- sliceBuffer(int) - Method in class Mask
-
- sliceBuffer(int) - Method in class BinaryVoxels
-
- sliceBuffer(int) - Method in interface SliceBufferIndex
-
- sliceBuffer(int) - Method in class Voxels
-
- sliceBufferGlobal(int) - Method in class BoundedVoxels
-
A slice buffer with global coordinates
- sliceBufferGlobal(int) - Method in class ObjectMask
-
A slice buffer with global coordinates
- SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.buffer.slice
-
A container with voxel-buffers for each z-slice.
- sliceBufferLocal(int) - Method in class ObjectWithProperties
-
- sliceBufferLocal(int) - Method in class BoundedVoxels
-
A slice buffer with local coordinates i.e.
- sliceBufferLocal(int) - Method in class ObjectMask
-
A slice buffer with local coordinates i.e.
- slices() - Method in class BinaryVoxels
-
- slices() - Method in class Voxels
-
- sliceStatisticsForRegion(VoxelizedMark, int) - Method in class IndexedRegionBase
-
- SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- SliceThresholder(BinaryValuesByte) - Constructor for class SliceThresholder
-
- SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class SliceThresholderMask
-
- SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class SliceThresholderWithoutMask
-
- SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer
-
Contains the buffer for the current slice, the current slice minus 1, and the current slice plus
1.
- SlidingBuffer(Voxels<T>) - Constructor for class SlidingBuffer
-
- Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
3x3 Sobel Filter
- Sobel() - Constructor for class Sobel
-
- solveQuadraticEquation(double, double, double) - Static method in class QuadraticEquationSolver
-
Solves a quadratic equation in form x^2 + b^x + c = 0
- sort(Comparator<Feature<T>>) - Method in class FeatureList
-
Creates a new feature-list sorted in a particular order.
- SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SortAlphabetically() - Constructor for class SortAlphabetically
-
- SortAlphabetically<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Sorts the input-items in alphabetical order of their input-name.
- SortAlphabetically() - Constructor for class SortAlphabetically
-
- SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SortAlphabeticallyWithDirectory() - Constructor for class SortAlphabeticallyWithDirectory
-
- SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Creates a new object-collection with objects sorted by a derived feature-value (in ascending
order)
- SortByFeature() - Constructor for class SortByFeature
-
- SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
-
- SortedSetChannel() - Constructor for class SortedSetChannel
-
- SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
-
- SortedSetSlice(String, int) - Constructor for class SortedSetSlice
-
- sourceVal - Variable in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- spatiallySeparate() - Method in class IntersectingObjects
-
Splits the collection of objects into spatially separate clusters.
- SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree
-
- SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class SpatiallySeparate
-
- SpatialUnits - Class in org.anchoranalysis.image.core.dimensions
-
Units to describe spatial quantities.
- SpatialUnits.UnitSuffix - Enum in org.anchoranalysis.image.core.dimensions
-
Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
- Specific - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- Specific() - Constructor for class Specific
-
- SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects a specific set of channels from stacks, each identified by a stack-name and channel index
- SpecificAndRename() - Constructor for class SpecificAndRename
-
- SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A feature based one one-specific principal-axis as identified by image moments.
- SpecificAxisBase() - Constructor for class SpecificAxisBase
-
- SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
- SpecificDisabled() - Constructor for class SpecificDisabled
-
- SpecificDisabled(StringSet) - Constructor for class SpecificDisabled
-
- SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are enabled.
- SpecificEnabled() - Constructor for class SpecificEnabled
-
- SpecificEnabled(StringSet) - Constructor for class SpecificEnabled
-
- SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- SpecificEnergyChannelBase() - Constructor for class SpecificEnergyChannelBase
-
- SpecificPathList - Class in org.anchoranalysis.io.input.bean.files
-
A specific list of paths which form the input.
- SpecificPathList(List<String>) - Constructor for class SpecificPathList
-
- SpecificPathList() - Constructor for class SpecificPathList
-
- SpecifyDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Specify dimensions via a bean.
- SpecifyDimensions(SizeXY) - Constructor for class SpecifyDimensions
-
Create with specific lengths for X and Y dimensions.
- SpecifyDimensions() - Constructor for class SpecifyDimensions
-
- Sphere - Class in org.anchoranalysis.mpp.mark.conic
-
A sphere
- Sphere(Bound) - Constructor for class Sphere
-
Creates with a radius within particular bounds.
- Sphere(Sphere) - Constructor for class Sphere
-
Copy Constructor
- Sphere() - Constructor for class Sphere
-
- split(Path) - Method in class RootPath
-
It splits the *root* portion of the path from the remainder
- split(Path, String, boolean) - Method in class RootPathMap
-
Given a path, it splits the *root* portion of the path from the remainder, trying a root
identified by the rootName and debugMode (and if this fails, also trying with
debugMode==false)
- SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
- SplitByObjects() - Constructor for class SplitByObjects
-
- SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean
-
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn"
points.
- SplitContourAtSaddlePoints() - Constructor for class SplitContourAtSaddlePoints
-
- splitFilename(String) - Static method in class ExtensionUtilities
-
Splits the file-name of a path into a base part and an extension part.
- SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
- SplitIntoSquares() - Constructor for class SplitIntoSquares
-
- SplitPath - Class in org.anchoranalysis.core.system.path
-
A path that has been split into two components: a root and a remainder.
- SplitPath(Path, Path) - Constructor for class SplitPath
-
- Stack - Class in org.anchoranalysis.image.core.stack
-
One or more single-channel images that all have the same dimensions.
- Stack(boolean) - Constructor for class Stack
-
- Stack() - Constructor for class Stack
-
- Stack(Channel) - Constructor for class Stack
-
- Stack(Dimensions, ChannelFactorySingleType, int, boolean) - Constructor for class Stack
-
- Stack(boolean, Channel...) - Constructor for class Stack
-
- Stack(Stream<Channel>) - Constructor for class Stack
-
- Stack(boolean, Stream<Channel>) - Constructor for class Stack
-
- stack() - Method in class MultiInput
-
- stack(String) - Static method in class ReferenceFactory
-
- StackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator
-
Writes a stack to the filesystem.
- StackGenerator(String, boolean) - Constructor for class StackGenerator
-
Creates a generator that performs no padding.
- StackGenerator(boolean, Optional<String>, boolean) - Constructor for class StackGenerator
-
Creates the generator from a stack, inferring whether all stacks will be 2D from this stack's
dimensions.
- StackGenerator(boolean, Optional<String>, StackWriteAttributes) - Constructor for class StackGenerator
-
- StackIdentifiers - Class in org.anchoranalysis.image.core.stack
-
- StackNotUniformSized - Class in org.anchoranalysis.image.core.stack
-
- StackNotUniformSized() - Constructor for class StackNotUniformSized
-
Creates an empty with no channels.
- StackNotUniformSized(Stream<Channel>) - Constructor for class StackNotUniformSized
-
- StackNotUniformSized(Channel) - Constructor for class StackNotUniformSized
-
- StackProvider - Class in org.anchoranalysis.image.bean.provider.stack
-
- StackProvider() - Constructor for class StackProvider
-
- StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack
-
- StackProviderUnary() - Constructor for class StackProviderUnary
-
- StackProviderWithLabel - Class in org.anchoranalysis.image.io.bean.stack.combine
-
- StackProviderWithLabel(Stack, String) - Constructor for class StackProviderWithLabel
-
- StackProviderWithLabel() - Constructor for class StackProviderWithLabel
-
- StackReader - Class in org.anchoranalysis.image.io.bean.stack.reader
-
Reads an image-
Stack from the file-system.
- StackReader() - Constructor for class StackReader
-
- stacks() - Method in class AnnotationWithStrategy
-
- stacks() - Method in class ImageInitialization
-
- STACKS - Static variable in class OutputterDirectories
-
Where stacks are typically placed in a define-experiment output
- Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
Each file gives either: * a single stack * a time-series of stacks
- Stacks(InputManager<FileInput>) - Constructor for class Stacks
-
- Stacks() - Constructor for class Stacks
-
- StackSequenceInput - Interface in org.anchoranalysis.image.io.stack.input
-
Provides a single stack (or a time series of such stacks) as an input
- StackSeries - Class in org.anchoranalysis.image.io.stack
-
- StackSeries() - Constructor for class StackSeries
-
- stackTrace() - Method in exception AnchorFriendlyCheckedException
-
Prints a stack trace of the current exception to a string
- StackWithMap - Class in org.anchoranalysis.mpp.io.input
-
Combines a Stack with a map of other stacks
- StackWithMap(String, ProvidesStackInput) - Constructor for class StackWithMap
-
- StackWriteAttributes - Class in org.anchoranalysis.image.io.stack.output
-
Attributes describing stack which may determine which writer is used.
- StackWriteAttributesFactory - Class in org.anchoranalysis.image.io.stack.output
-
- StackWriteOptions - Class in org.anchoranalysis.image.io.stack.output
-
A combination of attributions describing how to write a particular stack and any suggestions from
the user.
- StackWriteOptions(StackWriteAttributes, Optional<ImageFileFormat>) - Constructor for class StackWriteOptions
-
- StackWriter - Class in org.anchoranalysis.image.io.bean.stack.writer
-
Writes a stack (i.e.
- StackWriter() - Constructor for class StackWriter
-
- StackWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
- StackWriterDelegateBase() - Constructor for class StackWriterDelegateBase
-
- StandardDeviation - Class in org.anchoranalysis.feature.bean.results
-
The standard-deviation of the results from a particular feature.
- StandardDeviation() - Constructor for class StandardDeviation
-
- standardDeviation() - Method in class Histogram
-
- start() - Method in class StatefulNullMessageLogger
-
- start() - Method in class ConsoleMessageLogger
-
- start() - Method in class FailureOnlyMessageLogger
-
- start() - Method in class MessageLoggerList
-
- start() - Method in interface StatefulMessageLogger
-
- start() - Method in class TextFileMessageLogger
-
- start(FeatureInitialization, SharedFeatureMulti, Logger) - Method in class SequentialSession
-
Starts the session
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in interface FeatureTableCalculator
-
Initializes a feature store that has the same structure as that previously created by
createFeatures() from the same object
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class PairsTableCalculator
-
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class SingleTableCalculator
-
- start() - Method in class TextFileOutput
-
- start(EnergyStack) - Method in class CheckMark
-
- start(FeedbackBeginParameters<T>) - Method in class AggregateTriggerBank
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class DiscardOutliers
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class RelationWithMatches
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class GreaterIntersectionWith
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class IntensityGreaterEqualThan
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class IntersectsWith
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedFeature
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedVolume
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterPredicate
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterRelation
-
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class OutlinePreserveRelativeSize
-
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class ThumbnailFromObjects
-
Initializes a batch to create thumbnails.
- start() - Method in class ScaleToSize
-
- start() - Method in class ThumbnailFromStack
-
- start(EnergyStack) - Method in class AndList
-
- start(EnergyStack) - Method in class FeatureValueCheckMark
-
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class CombineObjectsForFeatures
-
Derives a list of inputs from an object-collection
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class EachObjectIndependently
-
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class PairNeighbors
-
- startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class ConvertImageFormat
-
- startSeries(S, U, InputOutputContext) - Method in class RasterTask
-
Starts processing of a series.
- startSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class MovieFromSlices
-
- StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log
-
A
MessageLogger that can be started and stopped, and is aware this state.
- StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log
-
Does nothing (i.e.
- StatefulNullMessageLogger() - Constructor for class StatefulNullMessageLogger
-
- StateReporter<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization
-
Converts the optimization state to a form that the reporter needs
- StateReporter() - Constructor for class StateReporter
-
- stateReporter() - Method in class AssignMode
-
- stateReporter() - Method in class DirectAssignMode
-
- stateReporter() - Method in class TransformationAssignMode
-
- StateReporterIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes the state is reported without any transformation
- StateReporterIdentity() - Constructor for class StateReporterIdentity
-
- StateReporterToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes we are interested in
VoxelizedMarksWithEnergy as reporting type, and our
optimization-state is in the form
ToPixelized<T>
- StateReporterToPixelized() - Constructor for class StateReporterToPixelized
-
- StateReporterTransformer<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
- StateReporterTransformer() - Constructor for class StateReporterTransformer
-
- stateToKernel() - Method in class KernelStateBridge
-
- stateToKernel() - Method in class KernelStateBridgeIdentity
-
- stateToKernel() - Method in class KernelStateBridgePixelize
-
- stateToKernel() - Method in class KernelStateBridgeTransformer
-
- StateTransformer<W,X> - Interface in org.anchoranalysis.mpp.segment.transformer
-
- StateTransformerBean<S,T> - Class in org.anchoranalysis.mpp.segment.transformer
-
Transforms one type into another
- StateTransformerBean() - Constructor for class StateTransformerBean
-
- StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
-
- StaticFilePath() - Constructor for class StaticFilePath
-
- StatisticalBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
-
Calculates a score based upon the statistical mean and std-deviation.
- StatisticalBase() - Constructor for class StatisticalBase
-
- StatisticForFeature - Class in org.anchoranalysis.feature.bean.results
-
Base class for calculating a statistic across all results in a
ResultsVectorList for a
particular feature.
- StatisticForFeature() - Constructor for class StatisticForFeature
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Mean
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Quantile
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class StandardDeviation
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class StatisticForFeature
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Sum
-
- statisticsFor(int, int, int) - Method in interface VoxelizedMark
-
- statisticsForAllSlices(int, int) - Method in interface VoxelizedMark
-
- statisticsForAllSlices(VoxelizedMark, boolean) - Method in class SelectSlicesWithIndexBase
-
- statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface VoxelizedMark
-
- stdDev() - Method in interface VoxelStatistics
-
- StdDev - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- StdDev() - Constructor for class StdDev
-
- Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
- Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class Steepest
-
- steepestDescent(Point3i, int, int) - Method in class Steepest
-
- StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store
-
Supplier of an object for a store
- stream() - Method in class StringSet
-
- stream() - Method in class StreamableCollection
-
- stream() - Method in class NameValueSet
-
- stream() - Method in class ResultsVectorList
-
- stream() - Method in class ObjectCollection
-
Provides various functional-programming operations on the object-collection
- stream() - Method in class BoundedList
-
A stream of elements in the list.
- StreamableCollection<T> - Class in org.anchoranalysis.core.functional
-
As a stream can only be used once, this data-structure allows for repeatedly getting streams from
a collection
- StreamableCollection(Collection<T>) - Constructor for class StreamableCollection
-
Create for a particular collection
- StreamableCollection(Supplier<Stream<T>>) - Constructor for class StreamableCollection
-
- streamAllObjects() - Method in class SegmentedObjects
-
Create a
Stream of
all contained objects,
including confidence.
- streamIndices(Collection<Integer>) - Method in class ObjectCollection
-
Streams only objects at specific indices.
- streamOverZ() - Method in class Extent
-
Streams over the range of z values
- streamStandardJava() - Method in class ObjectCollection
-
A stream of object-masks as per Java's standard collections interface
- StringBeanCollection - Interface in org.anchoranalysis.bean
-
A bean that provides a collection of Strings.
- StringGenerator - Class in org.anchoranalysis.io.generator.text
-
- StringGenerator() - Constructor for class StringGenerator
-
- StringList - Class in org.anchoranalysis.bean
-
A list of strings (order is defined).
- StringList() - Constructor for class StringList
-
- StringListFactory - Class in org.anchoranalysis.bean.xml.factory
-
- StringListFactory() - Constructor for class StringListFactory
-
- StringMap - Class in org.anchoranalysis.bean.shared
-
- StringMap() - Constructor for class StringMap
-
- StringMapItem - Class in org.anchoranalysis.bean.shared
-
A simple mapping from one string (source) to another (target)
- StringMapItem() - Constructor for class StringMapItem
-
- stringRepresentationForElement(int) - Method in interface IncompleteElementRange
-
Returns the typed-index corresponding to the integer-index.
- StringSet - Class in org.anchoranalysis.bean
-
A set of strings.
- StringSet(String...) - Constructor for class StringSet
-
- StringSet() - Constructor for class StringSet
-
- StringSetFactory - Class in org.anchoranalysis.bean.xml.factory
-
- StringSetFactory() - Constructor for class StringSetFactory
-
- StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- StringSuffixOutputNameStyle() - Constructor for class StringSuffixOutputNameStyle
-
- StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class StringSuffixOutputNameStyle
-
- StringsWithoutOrder - Class in org.anchoranalysis.io.manifest.sequencetype
-
A sequence of strings that has no order.
- StringsWithoutOrder() - Constructor for class StringsWithoutOrder
-
- StringUtilities - Class in org.anchoranalysis.core.value
-
Utility functions for manipualting strings.
- strMarks() - Method in class MarkWithPositionAndSingleRadius
-
- strPos() - Method in class MarkWithPosition
-
- subdirectories() - Method in class MutableDirectory
-
- Subdirectory - Class in org.anchoranalysis.io.manifest.directory
-
- Subdirectory(Path) - Constructor for class Subdirectory
-
- Subdirectory() - Constructor for class Subdirectory
-
- subdirectory(String, ManifestDirectoryDescription, boolean) - Method in interface InputOutputContext
-
Creates a new context that writes instead to a subdirectory.
- SubdirectoryBase - Class in org.anchoranalysis.io.manifest.directory
-
- SubdirectoryBase(Path) - Constructor for class SubdirectoryBase
-
- SubdirectoryBase() - Constructor for class SubdirectoryBase
-
- subdirectoryForGroupOutputs() - Method in class GroupedStackBase
-
An optional subdirectory where the group outputs are placed.
- subdirectoryForGroupOutputs() - Method in class ExportImageHistograms
-
- subdirectoryForGroupOutputs() - Method in class GroupedMeanChannelTask
-
- subList(int, int) - Method in class UpdatableMarksList
-
- SUBMARK_CORE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_CORE_INNER - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_INSIDE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_OUTSIDE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_SHELL - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_SHELL_OUTSIDE - Static variable in class GlobalRegionIdentifiers
-
- SubmittedJob - Class in org.anchoranalysis.experiment.task.processor
-
- SubmittedJob(JobDescription, JobState) - Constructor for class SubmittedJob
-
- subset(StringSet) - Method in class NamedStacks
-
Creates a new collection containing only items whose keys exist in a particular set
- subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class SharedFeatureMulti
-
Extracts the subset of inputs that are compatible with a particular input-type
- SubsetRangeIfRequested - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
If specified in the context, the existing name if subsetted according to an index range.
- SubsetRangeIfRequested() - Constructor for class SubsetRangeIfRequested
-
- subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class ColoredMarks
-
- subsetWhereBBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class ColoredOverlayCollection
-
- SubstituteRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
A regular expression substitution (replaceAll) is applied to the relative-path
- SubstituteRegularExpression() - Constructor for class SubstituteRegularExpression
-
- subtract(VarianceCalculator) - Method in class VarianceCalculator
-
- subtract(ReadableTuple3i) - Method in class Extent
-
- subtract(Tuple3d) - Method in class Tuple3d
-
- subtract(int) - Method in class Tuple3i
-
- subtract(ReadableTuple3i) - Method in class Tuple3i
-
- subtractFrom(int) - Method in interface VoxelsArithmetic
-
Subtracts all current voxel-values from a constant-value
- SubtractFrom<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- SubtractFrom() - Constructor for class SubtractFrom
-
- SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- SubtractFromConstant() - Constructor for class SubtractFromConstant
-
- subtractFromMaxValue() - Method in class VoxelsWrapper
-
- SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
- SubtractMean() - Constructor for class SubtractMean
-
- SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- SubtractReducedFromMerged() - Constructor for class SubtractReducedFromMerged
-
- SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Subtract second-object from first-object in a pair
- SubtractSecondFromFirst() - Constructor for class SubtractSecondFromFirst
-
- SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- SubtractTwoChannels(IntBinaryOperation) - Constructor for class SubtractTwoChannels
-
- suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
A string that describes the suffix for meters.
- SuggestionFormatException - Exception in org.anchoranalysis.image.core.dimensions.size.suggestion
-
- SuggestionFormatException(String) - Constructor for exception SuggestionFormatException
-
- Sum<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
- Sum(FeatureList<T>) - Constructor for class Sum
-
- Sum() - Constructor for class Sum
-
- Sum - Class in org.anchoranalysis.feature.bean.results
-
The sum of the results from a particular feature.
- Sum() - Constructor for class Sum
-
- sum() - Method in interface VoxelStatistics
-
- sum() - Method in class VoxelStatisticsCombined
-
- sum() - Method in class VoxelStatisticsFromHistogram
-
- sum() - Method in class AggIDCounter
-
- Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- Sum() - Constructor for class Sum
-
- summarize() - Method in exception BeanMisconfiguredXmlException
-
This summarize() option just looks for the most deep exception that can be 'combined' and
takes its message
- summarize() - Method in exception LocalisedBeanException
-
- summarize() - Method in exception AnchorCombinableException
-
- summarize() - Method in exception NamedProviderGetException
-
- SummarizeBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.task
-
- SummarizeBase() - Constructor for class SummarizeBase
-
- summarizeDisabled() - Method in class RecordedOutputs
-
A comma-separated string of all output-names that were not enabled.
- summarizeEnabled() - Method in class RecordedOutputs
-
A comma-separated string of all output-names that were enabled.
- summarizeIgnoreIdenticalFilePath(Path) - Method in exception LocalisedBeanException
-
If there is no nested-set of combinable exceptions, and the filenameDscr related to this
current exception, is identical as the passed parameter, then we simply ignore the
LocalisedBean and promote its getCause()
- SummarizeInputs<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task
-
- SummarizeInputs() - Constructor for class SummarizeInputs
-
- summarizeMultiplex(boolean) - Method in class RecordedOutputs
-
- Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Summarizes a set of elements by outputting a descriptive string
- Summarizer() - Constructor for class Summarizer
-
- SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Collects summary data about a set of input files that will eventually be outputted to the user
- SummarizerAggregate() - Constructor for class SummarizerAggregate
-
- SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
A count of the number of inputs.
- SummarizerCount() - Constructor for class SummarizerCount
-
- SummarizerInputFromManager<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
-
Extracts a particular item from an InputManager for summarization downstream
- SummarizerInputFromManager() - Constructor for class SummarizerInputFromManager
-
- SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Creates a string where each line is an element (the string representation thereof)
- SummarizerListMultiline() - Constructor for class SummarizerListMultiline
-
- SummarizerNamedChannels<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
- SummarizerNamedChannels() - Constructor for class SummarizerNamedChannels
-
- SummarizerNamedChannelsSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
A simple summerizer where there's one summary-item per image (series are ignored!)
- SummarizerNamedChannelsSimple() - Constructor for class SummarizerNamedChannelsSimple
-
- SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Multiplexes between two summarizers depending on the total number of count
- SummarizerSplitMoreThan() - Constructor for class SummarizerSplitMoreThan
-
- SummaryException - Exception in org.anchoranalysis.core.exception.combinable
-
A special kind of exception that represents a summary of an existing set of exceptions
- SummaryException(String, Throwable) - Constructor for exception SummaryException
-
- summaryStr() - Method in class Contour
-
- sumNonZero() - Method in class Histogram
-
- sumOfSquares() - Method in interface VoxelStatistics
-
- sumOfSquares() - Method in class VoxelStatisticsCombined
-
- sumOfSquares() - Method in class VoxelStatisticsFromHistogram
-
- sumOverlapFromPaired() - Method in class AssignmentOverlapFromPairs
-
- SupportsTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
- SupportsTimeSeries() - Constructor for class SupportsTimeSeries
-
- suppressedLogger() - Static method in class LoggingFixture
-
A
Logger that doesn't output anything
- suppressedMessageLogger() - Static method in class LoggingFixture
-
- SuppressNonMaxima<T> - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Applies a segmentation procedure followed by non-maxima suppression.
- SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>) - Constructor for class SuppressNonMaxima
-
Creates with a particular segmentation algorithm as an input.
- SuppressNonMaxima() - Constructor for class SuppressNonMaxima
-
- SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>, ReduceElements<ObjectMask>, boolean) - Constructor for class SuppressNonMaxima
-
- SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxel-faces along the surface (the faces of each voxel that touch outside)
- SurfaceNumberVoxelFaces() - Constructor for class SurfaceNumberVoxelFaces
-
- SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxels on the surface (all voxels on the exterior of the object)
- SurfaceNumberVoxels() - Constructor for class SurfaceNumberVoxels
-
- SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
- SurfaceNumberVoxelsBase() - Constructor for class SurfaceNumberVoxelsBase
-
- SurfaceSizeMaskNonZero - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- SurfaceSizeMaskNonZero() - Constructor for class SurfaceSizeMaskNonZero
-
- SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options
-
Treats the channel index as if it's time, and vice versa
- SwitchChannelTime() - Constructor for class SwitchChannelTime
-
- SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log
-
Switches between two log-reporters depending on whether detailed logging is switched on or not
- SwitchDetailedLogging() - Constructor for class SwitchDetailedLogging
-